Starting phenix.real_space_refine on Wed Aug 5 20:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.cif" model { file = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2026/8q6j_18188.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 81 5.16 5 C 7213 2.51 5 N 1969 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "C" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1657 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1665 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4794 Classifications: {'peptide': 624} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 579} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11535 At special positions: 0 Unit cell: (105.56, 129.92, 148.48, 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 81 16.00 O 2272 8.00 N 1969 7.00 C 7213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS D 216 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 170 " distance=2.03 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 202 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 222 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 246 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 320 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 453 " - pdb=" SG CYS E 482 " distance=2.03 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.02 Simple disulfide: pdb=" SG CYS E 493 " - pdb=" SG CYS E 506 " distance=2.02 Simple disulfide: pdb=" SG CYS E 509 " - pdb=" SG CYS E 518 " distance=2.03 Simple disulfide: pdb=" SG CYS E 522 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 545 " - pdb=" SG CYS E 562 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 574 " distance=2.02 Simple disulfide: pdb=" SG CYS E 578 " - pdb=" SG CYS E 601 " distance=2.03 Simple disulfide: pdb=" SG CYS E 604 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 612 " 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=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG E 701 " - " ASN E 46 " " NAG E 702 " - " ASN E 508 " " NAG E 703 " - " ASN E 549 " " NAG G 1 " - " ASN E 165 " " NAG J 1 " - " ASN E 237 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 582.1 milliseconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 9.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.982A pdb=" N GLY A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.025A pdb=" N ASP B 31 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 32 " --> pdb=" O ILE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.872A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.443A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.777A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.777A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.699A pdb=" N GLY D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.528A pdb=" N ASP E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.531A pdb=" N LEU E 52 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.514A pdb=" N ASP E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.860A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.962A pdb=" N CYS E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 4.083A pdb=" N CYS E 230 " --> pdb=" O HIS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 374 through 378 removed outlier: 4.254A pdb=" N VAL E 377 " --> pdb=" O GLN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 486 Processing helix chain 'E' and resid 493 through 497 removed outlier: 3.656A pdb=" N GLY E 496 " --> pdb=" O CYS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.720A pdb=" N GLN E 561 " --> pdb=" O GLU E 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 5.812A pdb=" N LEU A 46 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN A 37 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.641A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 150 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.673A pdb=" N THR B 117 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.095A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 188 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS B 171 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.095A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 184 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 176 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.750A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.602A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.509A pdb=" N TYR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 117 Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 150 removed outlier: 4.114A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.430A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.473A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.473A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 41 removed outlier: 5.252A pdb=" N GLY E 130 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 236 through 238 Processing sheet with id=AC6, first strand: chain 'E' and resid 250 through 252 Processing sheet with id=AC7, first strand: chain 'E' and resid 267 through 269 Processing sheet with id=AC8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 301 Processing sheet with id=AD1, first strand: chain 'E' and resid 320 through 321 removed outlier: 7.073A pdb=" N CYS E 320 " --> pdb=" O PHE E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD3, first strand: chain 'E' and resid 444 through 447 removed outlier: 3.692A pdb=" N LEU E 472 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE E 446 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 474 " --> pdb=" O ILE E 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 531 through 533 Processing sheet with id=AD5, first strand: chain 'E' and resid 568 through 570 Processing sheet with id=AD6, first strand: chain 'E' and resid 593 through 595 328 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3781 1.34 - 1.46: 2766 1.46 - 1.58: 5169 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11809 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C LEU E 43 " pdb=" N PRO E 44 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.25e-02 6.40e+03 4.60e+00 bond pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.36e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15791 2.38 - 4.77: 253 4.77 - 7.15: 30 7.15 - 9.54: 2 9.54 - 11.92: 2 Bond angle restraints: 16078 Sorted by residual: angle pdb=" N GLY D 97 " pdb=" CA GLY D 97 " pdb=" C GLY D 97 " ideal model delta sigma weight residual 112.34 104.64 7.70 2.04e+00 2.40e-01 1.42e+01 angle pdb=" C LEU E 423 " pdb=" N GLN E 424 " pdb=" CA GLN E 424 " ideal model delta sigma weight residual 122.37 128.82 -6.45 1.72e+00 3.38e-01 1.41e+01 angle pdb=" C VAL D 48 " pdb=" N ALA D 49 " pdb=" CA ALA D 49 " ideal model delta sigma weight residual 121.80 115.82 5.98 1.71e+00 3.42e-01 1.22e+01 angle pdb=" N THR E 422 " pdb=" CA THR E 422 " pdb=" C THR E 422 " ideal model delta sigma weight residual 110.80 103.50 7.30 2.13e+00 2.20e-01 1.17e+01 angle pdb=" CA LEU E 400 " pdb=" CB LEU E 400 " pdb=" CG LEU E 400 " ideal model delta sigma weight residual 116.30 128.22 -11.92 3.50e+00 8.16e-02 1.16e+01 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6494 17.88 - 35.76: 481 35.76 - 53.63: 90 53.63 - 71.51: 12 71.51 - 89.39: 6 Dihedral angle restraints: 7083 sinusoidal: 2778 harmonic: 4305 Sorted by residual: dihedral pdb=" CA PHE D 99A" pdb=" C PHE D 99A" pdb=" N TYR D 99B" pdb=" CA TYR D 99B" ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE E 446 " pdb=" C ILE E 446 " pdb=" N HIS E 447 " pdb=" CA HIS E 447 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU D 96 " pdb=" C LEU D 96 " pdb=" N GLY D 97 " pdb=" CA GLY D 97 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1408 0.054 - 0.107: 358 0.107 - 0.161: 46 0.161 - 0.215: 2 0.215 - 0.269: 3 Chirality restraints: 1817 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 549 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1814 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 502 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO E 503 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 503 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 503 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 124 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LEU D 124 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU D 124 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 125 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 148 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO D 149 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 234 2.60 - 3.18: 10479 3.18 - 3.75: 17642 3.75 - 4.33: 24425 4.33 - 4.90: 39705 Nonbonded interactions: 92485 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OD1 ASN E 46 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR E 422 " pdb=" OE1 GLN E 424 " model vdw 2.064 3.040 nonbonded pdb=" O LEU E 423 " pdb=" O HIS E 447 " model vdw 2.093 3.040 nonbonded pdb=" NH2 ARG E 434 " pdb=" O THR E 504 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP D 35 " pdb=" ND2 ASN D 95 " model vdw 2.098 3.120 ... (remaining 92480 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'C' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name SG )))) } ncs_group { reference = (chain 'B' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )))) selection = (chain 'D' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.007 0.085 11852 Z= 0.327 Angle : 0.767 11.919 16173 Z= 0.392 Chirality : 0.048 0.269 1817 Planarity : 0.006 0.059 2085 Dihedral : 12.795 89.390 4227 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.57 % Favored : 90.36 % Rotamer: Outliers : 5.69 % Allowed : 10.05 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.22), residues: 1484 helix: -1.46 (0.70), residues: 49 sheet: -0.60 (0.26), residues: 410 loop : -1.31 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 514 TYR 0.020 0.002 TYR E 389 PHE 0.020 0.002 PHE E 454 TRP 0.017 0.002 TRP E 393 HIS 0.005 0.001 HIS E 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.33 (11809) covalent geometry : angle 0.75847 / 0.39 (16078) SS BOND : bond 0.00468 / 0.26 ( 34) SS BOND : angle 1.11497 / 0.82 ( 68) hydrogen bonds : bond 0.13894 / 9.86 ( 299) hydrogen bonds : angle 7.14729 / 4.89 ( 783) link_BETA1-4 : bond 0.00669 / 0.34 ( 4) link_BETA1-4 : angle 1.52020 / 1.03 ( 12) link_NAG-ASN : bond 0.00616 / 0.44 ( 5) link_NAG-ASN : angle 3.14031 / 2.10 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 94 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 ASP cc_start: 0.8721 (m-30) cc_final: 0.8328 (m-30) REVERT: B 178 GLN cc_start: 0.2085 (mt0) cc_final: 0.1287 (mm110) REVERT: B 206 ASN cc_start: 0.7006 (t0) cc_final: 0.6647 (m-40) REVERT: C 75 ILE cc_start: 0.7840 (mm) cc_final: 0.7052 (tt) REVERT: C 81 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7709 (mp0) REVERT: C 199 GLN cc_start: 0.9011 (pt0) cc_final: 0.8787 (pm20) REVERT: E 71 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: E 95 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7960 (pp) REVERT: E 116 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7861 (ttm-80) REVERT: E 342 PHE cc_start: 0.7664 (m-80) cc_final: 0.7339 (m-80) REVERT: E 466 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8261 (p0) outliers start: 73 outliers final: 35 residues processed: 162 average time/residue: 0.1087 time to fit residues: 24.9420 Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 GLN A 147 GLN B 162 ASN B 171 HIS B 178 GLN C 37 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 210 ASN E 32 GLN E 37 ASN E 68 GLN E 227 HIS E 297 ASN E 416 ASN E 451 HIS E 462 GLN E 466 ASN E 511 GLN E 561 GLN E 624 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.106473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.074977 restraints weight = 45720.577| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 7.21 r_work: 0.3540 rms_B_bonded: 6.48 restraints_weight: 2.0000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11852 Z= 0.133 Angle : 0.662 9.877 16173 Z= 0.331 Chirality : 0.046 0.272 1817 Planarity : 0.005 0.077 2085 Dihedral : 7.402 59.085 1678 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 3.20 % Allowed : 13.33 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.22), residues: 1484 helix: -1.51 (0.65), residues: 46 sheet: -0.68 (0.24), residues: 446 loop : -0.91 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.013 0.002 TYR B 80 PHE 0.025 0.002 PHE D 122 TRP 0.009 0.001 TRP E 430 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11809) covalent geometry : angle 0.65246 / 0.33 (16078) SS BOND : bond 0.00491 / 0.26 ( 34) SS BOND : angle 1.06479 / 0.77 ( 68) hydrogen bonds : bond 0.03689 / 2.55 ( 299) hydrogen bonds : angle 6.07985 / 4.26 ( 783) link_BETA1-4 : bond 0.00572 / 0.30 ( 4) link_BETA1-4 : angle 1.76897 / 0.95 ( 12) link_NAG-ASN : bond 0.00570 / 0.41 ( 5) link_NAG-ASN : angle 2.83850 / 1.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8261 (ptm160) REVERT: C 75 ILE cc_start: 0.7810 (mm) cc_final: 0.7350 (tt) REVERT: C 81 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7622 (mp0) REVERT: C 179 LEU cc_start: 0.8451 (tp) cc_final: 0.8237 (tp) REVERT: E 95 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8010 (pp) REVERT: E 116 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7657 (ttm-80) REVERT: E 342 PHE cc_start: 0.7391 (m-80) cc_final: 0.7041 (m-80) REVERT: E 455 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.7057 (p) REVERT: E 465 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8221 (mmt-90) REVERT: E 466 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8326 (p0) REVERT: E 519 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7090 (p) outliers start: 41 outliers final: 23 residues processed: 104 average time/residue: 0.1034 time to fit residues: 15.8917 Evaluate side-chains 77 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 37 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.106649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.075290 restraints weight = 46805.807| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 6.57 r_work: 0.3552 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11852 Z= 0.116 Angle : 0.608 10.731 16173 Z= 0.301 Chirality : 0.045 0.263 1817 Planarity : 0.005 0.067 2085 Dihedral : 6.465 57.298 1648 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 2.65 % Allowed : 15.35 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1484 helix: -1.67 (0.63), residues: 46 sheet: -0.57 (0.24), residues: 451 loop : -0.85 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.012 0.001 TYR A 92 PHE 0.015 0.001 PHE A 139 TRP 0.009 0.001 TRP E 430 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11809) covalent geometry : angle 0.59945 / 0.30 (16078) SS BOND : bond 0.00265 / 0.14 ( 34) SS BOND : angle 0.85774 / 0.64 ( 68) hydrogen bonds : bond 0.03352 / 2.36 ( 299) hydrogen bonds : angle 5.82632 / 4.07 ( 783) link_BETA1-4 : bond 0.00771 / 0.40 ( 4) link_BETA1-4 : angle 1.54175 / 0.88 ( 12) link_NAG-ASN : bond 0.00587 / 0.45 ( 5) link_NAG-ASN : angle 2.83962 / 1.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7448 (mmm) cc_final: 0.6642 (mmm) REVERT: C 81 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7623 (mp0) REVERT: E 95 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (pp) REVERT: E 465 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8242 (mmt-90) REVERT: E 466 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8467 (p0) outliers start: 34 outliers final: 24 residues processed: 84 average time/residue: 0.0952 time to fit residues: 12.1852 Evaluate side-chains 68 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN E 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.103648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.071412 restraints weight = 46737.393| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 7.12 r_work: 0.3462 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11852 Z= 0.279 Angle : 0.712 9.227 16173 Z= 0.358 Chirality : 0.047 0.263 1817 Planarity : 0.005 0.075 2085 Dihedral : 6.796 59.573 1637 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.69 % Favored : 91.24 % Rotamer: Outliers : 4.29 % Allowed : 16.45 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1484 helix: -1.57 (0.65), residues: 46 sheet: -0.47 (0.25), residues: 421 loop : -1.12 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.021 0.002 TYR E 387 PHE 0.021 0.002 PHE E 454 TRP 0.015 0.002 TRP E 393 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 (11809) covalent geometry : angle 0.70336 / 0.36 (16078) SS BOND : bond 0.00386 / 0.21 ( 34) SS BOND : angle 1.16527 / 0.84 ( 68) hydrogen bonds : bond 0.04112 / 2.90 ( 299) hydrogen bonds : angle 6.14824 / 4.27 ( 783) link_BETA1-4 : bond 0.00763 / 0.39 ( 4) link_BETA1-4 : angle 1.62692 / 1.07 ( 12) link_NAG-ASN : bond 0.00548 / 0.40 ( 5) link_NAG-ASN : angle 2.94498 / 1.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 48 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7651 (mp0) REVERT: C 134 CYS cc_start: 0.6431 (t) cc_final: 0.5809 (t) REVERT: D 83 ARG cc_start: 0.8051 (mtm110) cc_final: 0.7851 (mtm110) REVERT: E 71 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8064 (pp30) REVERT: E 95 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (pp) REVERT: E 116 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7815 (ttm-80) REVERT: E 342 PHE cc_start: 0.7458 (m-80) cc_final: 0.7080 (m-80) REVERT: E 409 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7979 (tt) REVERT: E 466 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (p0) outliers start: 55 outliers final: 37 residues processed: 98 average time/residue: 0.1051 time to fit residues: 15.3005 Evaluate side-chains 83 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 41 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 chunk 83 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 37 ASN ** E 136 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 = 0.4360 r_free = 0.4360 target = 0.105916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.077390 restraints weight = 47530.630| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 5.98 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11852 Z= 0.113 Angle : 0.602 9.458 16173 Z= 0.299 Chirality : 0.045 0.255 1817 Planarity : 0.005 0.062 2085 Dihedral : 6.356 58.845 1637 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 3.82 % Allowed : 16.91 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1484 helix: -2.08 (0.58), residues: 53 sheet: -0.46 (0.25), residues: 432 loop : -0.92 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.001 TYR A 92 PHE 0.014 0.001 PHE A 139 TRP 0.013 0.001 TRP C 148 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11809) covalent geometry : angle 0.59400 / 0.30 (16078) SS BOND : bond 0.00269 / 0.13 ( 34) SS BOND : angle 0.83010 / 0.63 ( 68) hydrogen bonds : bond 0.03226 / 2.26 ( 299) hydrogen bonds : angle 5.81218 / 4.05 ( 783) link_BETA1-4 : bond 0.00682 / 0.36 ( 4) link_BETA1-4 : angle 1.47679 / 0.82 ( 12) link_NAG-ASN : bond 0.00554 / 0.42 ( 5) link_NAG-ASN : angle 2.77794 / 1.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 47 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7555 (mp0) REVERT: E 71 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: E 95 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8098 (pp) REVERT: E 116 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7603 (ttm-80) REVERT: E 466 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (p0) outliers start: 49 outliers final: 31 residues processed: 88 average time/residue: 0.1021 time to fit residues: 13.5638 Evaluate side-chains 76 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 41 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.105298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.073555 restraints weight = 46352.930| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 6.86 r_work: 0.3515 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11852 Z= 0.151 Angle : 0.605 9.415 16173 Z= 0.302 Chirality : 0.045 0.260 1817 Planarity : 0.005 0.060 2085 Dihedral : 6.150 51.433 1633 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 4.05 % Allowed : 17.23 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1484 helix: -2.02 (0.59), residues: 53 sheet: -0.45 (0.25), residues: 432 loop : -0.92 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 87 TYR 0.014 0.001 TYR A 92 PHE 0.012 0.001 PHE A 139 TRP 0.014 0.001 TRP C 148 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (11809) covalent geometry : angle 0.59589 / 0.30 (16078) SS BOND : bond 0.00331 / 0.16 ( 34) SS BOND : angle 1.01987 / 0.78 ( 68) hydrogen bonds : bond 0.03299 / 2.31 ( 299) hydrogen bonds : angle 5.81008 / 4.06 ( 783) link_BETA1-4 : bond 0.00764 / 0.40 ( 4) link_BETA1-4 : angle 1.43258 / 0.87 ( 12) link_NAG-ASN : bond 0.00533 / 0.42 ( 5) link_NAG-ASN : angle 2.83810 / 1.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 46 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7717 (mmm) cc_final: 0.6279 (mmm) REVERT: B 87 ARG cc_start: 0.7109 (ptp90) cc_final: 0.6901 (ptp90) REVERT: C 81 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7671 (mp0) REVERT: E 71 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8050 (pp30) REVERT: E 95 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8204 (pp) REVERT: E 116 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7629 (ttm-80) REVERT: E 466 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8708 (p0) outliers start: 52 outliers final: 38 residues processed: 87 average time/residue: 0.0873 time to fit residues: 11.5839 Evaluate side-chains 84 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 42 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 147 optimal weight: 0.0670 chunk 119 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.103550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.071680 restraints weight = 46847.131| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 6.21 r_work: 0.3477 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11852 Z= 0.267 Angle : 0.703 9.258 16173 Z= 0.355 Chirality : 0.047 0.255 1817 Planarity : 0.005 0.064 2085 Dihedral : 6.629 57.436 1632 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 4.68 % Allowed : 17.77 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.22), residues: 1484 helix: -2.19 (0.56), residues: 59 sheet: -0.40 (0.26), residues: 409 loop : -1.22 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.020 0.002 TYR E 387 PHE 0.024 0.002 PHE D 100 TRP 0.015 0.002 TRP E 393 HIS 0.007 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.27 (11809) covalent geometry : angle 0.69378 / 0.35 (16078) SS BOND : bond 0.00374 / 0.20 ( 34) SS BOND : angle 1.24190 / 0.92 ( 68) hydrogen bonds : bond 0.03932 / 2.75 ( 299) hydrogen bonds : angle 6.12562 / 4.26 ( 783) link_BETA1-4 : bond 0.00663 / 0.34 ( 4) link_BETA1-4 : angle 1.55917 / 1.02 ( 12) link_NAG-ASN : bond 0.00539 / 0.39 ( 5) link_NAG-ASN : angle 2.93105 / 1.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 40 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7776 (mmm) cc_final: 0.6072 (mmm) REVERT: C 81 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7674 (mp0) REVERT: C 143 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: D 66 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5042 (ptm160) REVERT: E 71 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8218 (pp30) REVERT: E 95 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8471 (pp) REVERT: E 116 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8112 (ttm-80) outliers start: 60 outliers final: 44 residues processed: 89 average time/residue: 0.0800 time to fit residues: 11.2007 Evaluate side-chains 89 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 40 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.0970 chunk 35 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.105836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.074419 restraints weight = 45878.572| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 6.62 r_work: 0.3535 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11852 Z= 0.111 Angle : 0.598 9.505 16173 Z= 0.298 Chirality : 0.045 0.257 1817 Planarity : 0.005 0.059 2085 Dihedral : 6.123 59.154 1630 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 3.43 % Allowed : 19.17 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1484 helix: -1.82 (0.64), residues: 53 sheet: -0.49 (0.25), residues: 436 loop : -0.88 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.026 0.001 TYR A 92 PHE 0.012 0.001 PHE A 139 TRP 0.013 0.001 TRP E 430 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11809) covalent geometry : angle 0.58948 / 0.30 (16078) SS BOND : bond 0.00254 / 0.13 ( 34) SS BOND : angle 0.94884 / 0.73 ( 68) hydrogen bonds : bond 0.03074 / 2.14 ( 299) hydrogen bonds : angle 5.77618 / 4.05 ( 783) link_BETA1-4 : bond 0.00715 / 0.37 ( 4) link_BETA1-4 : angle 1.44043 / 0.79 ( 12) link_NAG-ASN : bond 0.00564 / 0.43 ( 5) link_NAG-ASN : angle 2.71400 / 1.83 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 46 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7699 (mp0) REVERT: C 143 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: E 71 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8085 (pp30) REVERT: E 95 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8296 (pp) outliers start: 44 outliers final: 39 residues processed: 81 average time/residue: 0.0765 time to fit residues: 9.6402 Evaluate side-chains 84 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.104115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.072823 restraints weight = 46252.596| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 6.09 r_work: 0.3539 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11852 Z= 0.212 Angle : 0.667 9.306 16173 Z= 0.335 Chirality : 0.046 0.258 1817 Planarity : 0.005 0.061 2085 Dihedral : 6.391 56.985 1630 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 3.90 % Allowed : 19.10 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.22), residues: 1484 helix: -2.02 (0.60), residues: 59 sheet: -0.47 (0.25), residues: 423 loop : -1.08 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 87 TYR 0.019 0.002 TYR E 387 PHE 0.019 0.002 PHE D 100 TRP 0.012 0.002 TRP E 393 HIS 0.006 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (11809) covalent geometry : angle 0.65832 / 0.33 (16078) SS BOND : bond 0.00316 / 0.17 ( 34) SS BOND : angle 1.07952 / 0.80 ( 68) hydrogen bonds : bond 0.03568 / 2.49 ( 299) hydrogen bonds : angle 5.92778 / 4.14 ( 783) link_BETA1-4 : bond 0.00721 / 0.37 ( 4) link_BETA1-4 : angle 1.47780 / 0.93 ( 12) link_NAG-ASN : bond 0.00518 / 0.39 ( 5) link_NAG-ASN : angle 2.85521 / 1.88 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 43 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7639 (mmm) cc_final: 0.6208 (mmm) REVERT: C 81 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7755 (mp0) REVERT: C 143 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: D 18 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8193 (tt) REVERT: E 71 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8368 (pp30) REVERT: E 95 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8588 (pp) outliers start: 50 outliers final: 42 residues processed: 84 average time/residue: 0.0908 time to fit residues: 12.1319 Evaluate side-chains 86 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 40 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.104356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.072572 restraints weight = 46100.101| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 6.55 r_work: 0.3475 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11852 Z= 0.181 Angle : 0.642 9.340 16173 Z= 0.321 Chirality : 0.045 0.253 1817 Planarity : 0.005 0.063 2085 Dihedral : 6.350 55.940 1630 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 3.74 % Allowed : 19.56 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.22), residues: 1484 helix: -2.05 (0.59), residues: 59 sheet: -0.64 (0.25), residues: 444 loop : -1.03 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 67 TYR 0.019 0.002 TYR A 92 PHE 0.015 0.002 PHE D 100 TRP 0.013 0.001 TRP E 430 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (11809) covalent geometry : angle 0.63325 / 0.32 (16078) SS BOND : bond 0.00288 / 0.15 ( 34) SS BOND : angle 1.03406 / 0.78 ( 68) hydrogen bonds : bond 0.03414 / 2.37 ( 299) hydrogen bonds : angle 5.88771 / 4.12 ( 783) link_BETA1-4 : bond 0.00667 / 0.34 ( 4) link_BETA1-4 : angle 1.42832 / 0.83 ( 12) link_NAG-ASN : bond 0.00511 / 0.39 ( 5) link_NAG-ASN : angle 2.77900 / 1.84 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 44 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7706 (mmm) cc_final: 0.6227 (mmm) REVERT: C 81 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7736 (mp0) REVERT: C 143 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: D 18 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8218 (tt) REVERT: E 71 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8327 (pp30) REVERT: E 95 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (pp) outliers start: 48 outliers final: 43 residues processed: 83 average time/residue: 0.0893 time to fit residues: 11.7883 Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 43 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.104397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.072585 restraints weight = 46652.214| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 6.69 r_work: 0.3473 rms_B_bonded: 6.27 restraints_weight: 2.0000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 11852 Z= 0.244 Angle : 0.901 59.196 16173 Z= 0.511 Chirality : 0.046 0.355 1817 Planarity : 0.005 0.069 2085 Dihedral : 6.396 56.012 1630 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.68 % Favored : 92.18 % Rotamer: Outliers : 3.90 % Allowed : 19.33 % Favored : 76.77 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.22), residues: 1484 helix: -2.05 (0.59), residues: 59 sheet: -0.64 (0.25), residues: 444 loop : -1.03 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.017 0.002 TYR A 92 PHE 0.015 0.002 PHE D 100 TRP 0.013 0.001 TRP E 430 HIS 0.005 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (11809) covalent geometry : angle 0.89461 / 0.51 (16078) SS BOND : bond 0.00294 / 0.15 ( 34) SS BOND : angle 1.27831 / 0.81 ( 68) hydrogen bonds : bond 0.03468 / 2.41 ( 299) hydrogen bonds : angle 5.85730 / 4.09 ( 783) link_BETA1-4 : bond 0.00863 / 0.45 ( 4) link_BETA1-4 : angle 1.46454 / 0.91 ( 12) link_NAG-ASN : bond 0.00512 / 0.40 ( 5) link_NAG-ASN : angle 2.77921 / 1.84 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.64 seconds wall clock time: 69 minutes 39.82 seconds (4179.82 seconds total)