Starting phenix.real_space_refine on Sat Aug 23 11:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_18188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_18188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_18188.map" model { file = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_18188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6j_18188/08_2025/8q6j_18188.cif" } 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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.92, per 1000 atoms: 0.25 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: 0.82 Conformation dependent library (CDL) restraints added in 580.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 2.26 Time building geometry restraints manager: 1.16 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 - 23.60: 6871 23.60 - 47.20: 317 47.20 - 70.80: 49 70.80 - 94.41: 17 94.41 - 118.01: 14 Dihedral angle restraints: 7268 sinusoidal: 2963 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 7265 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: 2.190 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 15.115 118.008 4412 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 aren 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 covalent geometry : bond 0.00703 (11809) covalent geometry : angle 0.75847 (16078) SS BOND : bond 0.00468 ( 34) SS BOND : angle 1.11497 ( 68) hydrogen bonds : bond 0.13894 ( 299) hydrogen bonds : angle 7.14729 ( 783) link_BETA1-4 : bond 0.00669 ( 4) link_BETA1-4 : angle 1.52020 ( 12) link_NAG-ASN : bond 0.00616 ( 5) link_NAG-ASN : angle 3.14031 ( 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 : 0.426 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: 0.1141 time to fit residues: 25.8969 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 : 0.440 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 147 GLN B 162 ASN B 171 HIS B 178 GLN C 37 GLN C 166 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.106450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.075501 restraints weight = 45705.988| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 6.31 r_work: 0.3530 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1492 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= 0.126 Angle : 0.670 10.020 16173 Z= 0.330 Chirality : 0.046 0.254 1817 Planarity : 0.005 0.075 2085 Dihedral : 11.873 101.565 1863 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 3.27 % Allowed : 13.17 % Favored : 83.55 % 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 aren not related in a simple way. whole: -1.30 (0.22), residues: 1484 helix: -1.70 (0.62), residues: 52 sheet: -0.65 (0.24), residues: 445 loop : -0.91 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 142 TYR 0.012 0.002 TYR B 80 PHE 0.026 0.001 PHE D 122 TRP 0.009 0.001 TRP E 430 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00277 (11809) covalent geometry : angle 0.65927 (16078) SS BOND : bond 0.00336 ( 34) SS BOND : angle 0.96632 ( 68) hydrogen bonds : bond 0.03583 ( 299) hydrogen bonds : angle 6.06814 ( 783) link_BETA1-4 : bond 0.00717 ( 4) link_BETA1-4 : angle 2.65766 ( 12) link_NAG-ASN : bond 0.00556 ( 5) link_NAG-ASN : angle 2.92142 ( 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 107 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8271 (ptm160) REVERT: B 151 ASP cc_start: 0.8705 (m-30) cc_final: 0.8411 (t0) REVERT: C 75 ILE cc_start: 0.7700 (mm) cc_final: 0.7255 (tt) REVERT: C 81 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7611 (mp0) REVERT: C 148 TRP cc_start: 0.5521 (m100) cc_final: 0.5298 (m100) REVERT: C 179 LEU cc_start: 0.8449 (tp) cc_final: 0.8232 (tp) REVERT: D 35 ASP cc_start: 0.7733 (m-30) cc_final: 0.7508 (m-30) REVERT: D 85 GLU cc_start: 0.8658 (pp20) cc_final: 0.8412 (pp20) REVERT: E 95 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8006 (pp) REVERT: E 116 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7632 (ttm-80) REVERT: E 342 PHE cc_start: 0.7389 (m-80) cc_final: 0.7039 (m-80) REVERT: E 455 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.7068 (p) REVERT: E 465 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8223 (mmt-90) REVERT: E 466 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8326 (p0) REVERT: E 519 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7069 (p) outliers start: 42 outliers final: 23 residues processed: 101 average time/residue: 0.1101 time to fit residues: 16.2177 Evaluate side-chains 79 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.0370 chunk 87 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.074531 restraints weight = 46168.874| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 7.07 r_work: 0.3539 rms_B_bonded: 6.49 restraints_weight: 2.0000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1771 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= 0.130 Angle : 0.623 10.379 16173 Z= 0.305 Chirality : 0.045 0.264 1817 Planarity : 0.005 0.070 2085 Dihedral : 10.361 97.145 1833 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 3.43 % Allowed : 15.04 % Favored : 81.53 % 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 aren not related in a simple way. whole: -1.19 (0.22), residues: 1484 helix: -1.55 (0.64), residues: 46 sheet: -0.52 (0.25), residues: 438 loop : -0.88 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.011 0.001 TYR A 92 PHE 0.014 0.001 PHE A 139 TRP 0.009 0.001 TRP E 430 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00291 (11809) covalent geometry : angle 0.61187 (16078) SS BOND : bond 0.00285 ( 34) SS BOND : angle 0.90479 ( 68) hydrogen bonds : bond 0.03434 ( 299) hydrogen bonds : angle 5.84565 ( 783) link_BETA1-4 : bond 0.00728 ( 4) link_BETA1-4 : angle 2.46692 ( 12) link_NAG-ASN : bond 0.00564 ( 5) link_NAG-ASN : angle 2.96170 ( 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 101 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 57 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8261 (ptm160) REVERT: C 81 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7614 (mp0) REVERT: C 179 LEU cc_start: 0.8457 (tp) cc_final: 0.8237 (tp) REVERT: D 83 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8134 (mtm110) REVERT: E 71 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7951 (pp30) REVERT: E 95 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8054 (pp) REVERT: E 116 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7711 (ttm-80) REVERT: E 409 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7866 (tt) REVERT: E 455 VAL cc_start: 0.7119 (OUTLIER) cc_final: 0.6847 (p) REVERT: E 465 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8251 (mmt-90) REVERT: E 466 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (p0) outliers start: 44 outliers final: 27 residues processed: 95 average time/residue: 0.1017 time to fit residues: 14.0994 Evaluate side-chains 83 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 48 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 185 LEU 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 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 131 THR Chi-restraints excluded: chain D residue 193 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 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 549 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN E 37 ASN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.101914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.069480 restraints weight = 47123.035| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 7.26 r_work: 0.3410 rms_B_bonded: 6.39 restraints_weight: 2.0000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 11852 Z= 0.389 Angle : 0.852 11.214 16173 Z= 0.428 Chirality : 0.050 0.261 1817 Planarity : 0.006 0.082 2085 Dihedral : 10.421 97.689 1829 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.24 % Favored : 89.69 % Rotamer: Outliers : 5.07 % Allowed : 16.68 % Favored : 78.25 % 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 aren not related in a simple way. whole: -1.79 (0.22), residues: 1484 helix: -1.94 (0.59), residues: 58 sheet: -0.68 (0.25), residues: 419 loop : -1.43 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 83 TYR 0.027 0.003 TYR E 389 PHE 0.026 0.003 PHE E 454 TRP 0.021 0.003 TRP E 393 HIS 0.008 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00853 (11809) covalent geometry : angle 0.84080 (16078) SS BOND : bond 0.00479 ( 34) SS BOND : angle 1.43633 ( 68) hydrogen bonds : bond 0.04819 ( 299) hydrogen bonds : angle 6.55215 ( 783) link_BETA1-4 : bond 0.00830 ( 4) link_BETA1-4 : angle 2.59656 ( 12) link_NAG-ASN : bond 0.00635 ( 5) link_NAG-ASN : angle 3.14420 ( 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 112 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 47 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7658 (mp0) REVERT: D 66 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.4405 (ptm160) REVERT: D 83 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8059 (mtm180) REVERT: E 71 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8201 (pp30) REVERT: E 95 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7983 (pp) REVERT: E 342 PHE cc_start: 0.7499 (m-80) cc_final: 0.7170 (m-80) REVERT: E 466 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8637 (p0) outliers start: 65 outliers final: 42 residues processed: 109 average time/residue: 0.0958 time to fit residues: 15.4989 Evaluate side-chains 85 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 39 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 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 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 33 THR 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 187 SER 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 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 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 Chi-restraints excluded: chain E residue 563 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** 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 = 0.4351 r_free = 0.4351 target = 0.105656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.077140 restraints weight = 47463.374| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 5.83 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2188 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= 0.117 Angle : 0.639 11.693 16173 Z= 0.314 Chirality : 0.045 0.249 1817 Planarity : 0.005 0.067 2085 Dihedral : 9.363 89.956 1825 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 4.05 % Allowed : 18.47 % Favored : 77.47 % 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 aren not related in a simple way. whole: -1.28 (0.22), residues: 1484 helix: -2.06 (0.59), residues: 53 sheet: -0.32 (0.26), residues: 408 loop : -1.04 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.023 0.001 TYR A 92 PHE 0.017 0.001 PHE A 139 TRP 0.014 0.001 TRP E 430 HIS 0.013 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00260 (11809) covalent geometry : angle 0.62872 (16078) SS BOND : bond 0.00266 ( 34) SS BOND : angle 0.98235 ( 68) hydrogen bonds : bond 0.03375 ( 299) hydrogen bonds : angle 5.96409 ( 783) link_BETA1-4 : bond 0.00594 ( 4) link_BETA1-4 : angle 2.25844 ( 12) link_NAG-ASN : bond 0.00526 ( 5) link_NAG-ASN : angle 2.87957 ( 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 100 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 48 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7436 (mmm) cc_final: 0.6003 (mmm) REVERT: B 98 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7789 (ptm160) REVERT: C 81 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7640 (mp0) REVERT: C 179 LEU cc_start: 0.8542 (tp) cc_final: 0.8238 (mt) REVERT: E 71 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7862 (pp30) REVERT: E 95 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8105 (pp) REVERT: E 465 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (mmt-90) REVERT: E 466 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8720 (p0) outliers start: 52 outliers final: 34 residues processed: 94 average time/residue: 0.0939 time to fit residues: 13.2860 Evaluate side-chains 82 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET 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 134 CYS Chi-restraints excluded: chain C residue 136 LEU 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 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 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 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 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 490 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4332 r_free = 0.4332 target = 0.103945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.072282 restraints weight = 46517.037| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 6.50 r_work: 0.3476 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2234 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= 0.199 Angle : 0.671 12.041 16173 Z= 0.330 Chirality : 0.045 0.259 1817 Planarity : 0.005 0.064 2085 Dihedral : 8.877 77.941 1823 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.49 % Favored : 91.44 % Rotamer: Outliers : 4.21 % Allowed : 19.02 % Favored : 76.77 % 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 aren not related in a simple way. whole: -1.44 (0.22), residues: 1484 helix: -2.35 (0.54), residues: 59 sheet: -0.39 (0.26), residues: 410 loop : -1.15 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.023 0.002 TYR A 92 PHE 0.016 0.002 PHE E 454 TRP 0.015 0.002 TRP E 393 HIS 0.013 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00442 (11809) covalent geometry : angle 0.65896 (16078) SS BOND : bond 0.00396 ( 34) SS BOND : angle 1.03283 ( 68) hydrogen bonds : bond 0.03675 ( 299) hydrogen bonds : angle 5.98847 ( 783) link_BETA1-4 : bond 0.00613 ( 4) link_BETA1-4 : angle 2.40144 ( 12) link_NAG-ASN : bond 0.00553 ( 5) link_NAG-ASN : angle 3.17866 ( 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 96 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 42 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7713 (mmm) cc_final: 0.6630 (mmm) REVERT: A 75 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 81 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7667 (mp0) REVERT: C 179 LEU cc_start: 0.8398 (tp) cc_final: 0.8136 (mt) REVERT: E 71 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8048 (pp30) REVERT: E 95 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8123 (pp) outliers start: 54 outliers final: 39 residues processed: 86 average time/residue: 0.0927 time to fit residues: 12.1690 Evaluate side-chains 81 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 39 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE 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 204 ASN 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 134 CYS 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 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 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 71 GLN Chi-restraints excluded: chain E residue 95 LEU 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 433 LEU Chi-restraints excluded: chain E residue 465 ARG 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: 3.9990 chunk 16 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 147 optimal weight: 0.0470 chunk 119 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.104190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.072802 restraints weight = 46831.369| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 6.37 r_work: 0.3536 rms_B_bonded: 6.00 restraints_weight: 2.0000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2397 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= 0.190 Angle : 0.657 11.431 16173 Z= 0.324 Chirality : 0.045 0.253 1817 Planarity : 0.005 0.062 2085 Dihedral : 7.876 59.469 1821 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.68 % Favored : 92.25 % Rotamer: Outliers : 4.44 % Allowed : 19.17 % Favored : 76.38 % 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 aren not related in a simple way. whole: -1.44 (0.22), residues: 1484 helix: -2.31 (0.57), residues: 59 sheet: -0.42 (0.26), residues: 410 loop : -1.14 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 116 TYR 0.021 0.002 TYR A 92 PHE 0.013 0.002 PHE D 146 TRP 0.012 0.002 TRP E 430 HIS 0.012 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00421 (11809) covalent geometry : angle 0.64333 (16078) SS BOND : bond 0.00296 ( 34) SS BOND : angle 1.00110 ( 68) hydrogen bonds : bond 0.03595 ( 299) hydrogen bonds : angle 5.97194 ( 783) link_BETA1-4 : bond 0.00625 ( 4) link_BETA1-4 : angle 2.46818 ( 12) link_NAG-ASN : bond 0.00591 ( 5) link_NAG-ASN : angle 3.48012 ( 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 102 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 45 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: C 81 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7713 (mp0) REVERT: C 179 LEU cc_start: 0.8532 (tp) cc_final: 0.8233 (mt) REVERT: E 71 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: E 95 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8575 (pp) REVERT: E 465 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8430 (mmt-90) outliers start: 57 outliers final: 44 residues processed: 95 average time/residue: 0.1006 time to fit residues: 14.2408 Evaluate side-chains 89 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 41 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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 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 38 GLN 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 134 CYS Chi-restraints excluded: chain C residue 136 LEU 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 33 THR 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 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 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 465 ARG Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 490 HIS 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: 0.3980 chunk 35 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4347 r_free = 0.4347 target = 0.103947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.072732 restraints weight = 46729.657| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 6.42 r_work: 0.3531 rms_B_bonded: 6.04 restraints_weight: 2.0000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11852 Z= 0.195 Angle : 0.661 9.637 16173 Z= 0.328 Chirality : 0.045 0.256 1817 Planarity : 0.005 0.060 2085 Dihedral : 7.562 59.504 1821 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.29 % Favored : 91.64 % Rotamer: Outliers : 4.21 % Allowed : 19.72 % Favored : 76.07 % 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 aren not related in a simple way. whole: -1.46 (0.22), residues: 1484 helix: -2.32 (0.58), residues: 59 sheet: -0.44 (0.26), residues: 410 loop : -1.16 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.021 0.002 TYR A 92 PHE 0.014 0.002 PHE E 454 TRP 0.013 0.002 TRP E 393 HIS 0.012 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00434 (11809) covalent geometry : angle 0.64689 (16078) SS BOND : bond 0.00310 ( 34) SS BOND : angle 1.00677 ( 68) hydrogen bonds : bond 0.03606 ( 299) hydrogen bonds : angle 5.99494 ( 783) link_BETA1-4 : bond 0.00690 ( 4) link_BETA1-4 : angle 2.42072 ( 12) link_NAG-ASN : bond 0.00595 ( 5) link_NAG-ASN : angle 3.67937 ( 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 95 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 41 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7485 (mmm) cc_final: 0.6296 (mmm) REVERT: C 38 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: C 81 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7685 (mp0) REVERT: C 179 LEU cc_start: 0.8529 (tp) cc_final: 0.8227 (mt) REVERT: E 71 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8262 (pp30) REVERT: E 95 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 465 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8402 (mmt-90) outliers start: 54 outliers final: 44 residues processed: 88 average time/residue: 0.0963 time to fit residues: 12.8550 Evaluate side-chains 88 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 40 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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 38 GLN 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 134 CYS Chi-restraints excluded: chain C residue 136 LEU 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 33 THR 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 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 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 465 ARG Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 490 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.103947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.072887 restraints weight = 46069.601| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 6.18 r_work: 0.3527 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2615 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= 0.193 Angle : 0.659 9.548 16173 Z= 0.328 Chirality : 0.045 0.254 1817 Planarity : 0.005 0.061 2085 Dihedral : 7.390 59.463 1821 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.98 % Rotamer: Outliers : 4.68 % Allowed : 19.72 % Favored : 75.60 % 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 aren not related in a simple way. whole: -1.45 (0.22), residues: 1484 helix: -2.24 (0.60), residues: 57 sheet: -0.46 (0.25), residues: 419 loop : -1.14 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 477 TYR 0.021 0.002 TYR B 201 PHE 0.013 0.002 PHE D 100 TRP 0.013 0.002 TRP E 430 HIS 0.012 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00429 (11809) covalent geometry : angle 0.64477 (16078) SS BOND : bond 0.00290 ( 34) SS BOND : angle 1.01072 ( 68) hydrogen bonds : bond 0.03595 ( 299) hydrogen bonds : angle 6.00394 ( 783) link_BETA1-4 : bond 0.00605 ( 4) link_BETA1-4 : angle 2.53808 ( 12) link_NAG-ASN : bond 0.00557 ( 5) link_NAG-ASN : angle 3.50126 ( 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 102 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 42 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7461 (mmm) cc_final: 0.6349 (mmm) REVERT: C 38 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: C 179 LEU cc_start: 0.8515 (tp) cc_final: 0.8212 (mt) REVERT: E 71 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8218 (pp30) REVERT: E 95 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8586 (pp) outliers start: 60 outliers final: 50 residues processed: 94 average time/residue: 0.0917 time to fit residues: 13.1355 Evaluate side-chains 92 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 39 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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 204 ASN 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 38 GLN 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 134 CYS Chi-restraints excluded: chain C residue 136 LEU 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 33 THR 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 135 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 16 SER 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 197 VAL 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 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 465 ARG 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 20 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.104138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.073352 restraints weight = 46325.541| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 6.02 r_work: 0.3541 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2714 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= 0.174 Angle : 0.644 9.543 16173 Z= 0.320 Chirality : 0.045 0.254 1817 Planarity : 0.005 0.058 2085 Dihedral : 7.265 59.789 1821 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.75 % Favored : 92.18 % Rotamer: Outliers : 4.05 % Allowed : 20.27 % Favored : 75.68 % 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 aren not related in a simple way. whole: -1.41 (0.22), residues: 1484 helix: -2.23 (0.59), residues: 57 sheet: -0.48 (0.25), residues: 421 loop : -1.09 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.019 0.002 TYR A 92 PHE 0.012 0.002 PHE E 512 TRP 0.012 0.001 TRP E 430 HIS 0.013 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00388 (11809) covalent geometry : angle 0.63099 (16078) SS BOND : bond 0.00294 ( 34) SS BOND : angle 0.96101 ( 68) hydrogen bonds : bond 0.03467 ( 299) hydrogen bonds : angle 5.94445 ( 783) link_BETA1-4 : bond 0.00558 ( 4) link_BETA1-4 : angle 2.57660 ( 12) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 3.33863 ( 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 96 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 44 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7503 (mmm) cc_final: 0.6356 (mmm) REVERT: C 179 LEU cc_start: 0.8549 (tp) cc_final: 0.8241 (mt) REVERT: E 71 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8193 (pp30) REVERT: E 95 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8528 (pp) REVERT: E 465 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8452 (mmt-90) outliers start: 52 outliers final: 46 residues processed: 89 average time/residue: 0.0932 time to fit residues: 12.6456 Evaluate side-chains 91 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 42 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN 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 204 ASN 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 134 CYS Chi-restraints excluded: chain C residue 136 LEU 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 33 THR 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 135 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 16 SER 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 197 VAL 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 385 THR Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 465 ARG 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 68 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4364 r_free = 0.4364 target = 0.104816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.074054 restraints weight = 47008.587| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 5.98 r_work: 0.3557 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2838 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= 0.139 Angle : 0.620 10.043 16173 Z= 0.307 Chirality : 0.044 0.254 1817 Planarity : 0.005 0.052 2085 Dihedral : 7.089 59.750 1821 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 4.36 % Allowed : 19.88 % Favored : 75.76 % 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 aren not related in a simple way. whole: -1.32 (0.23), residues: 1484 helix: -2.11 (0.60), residues: 57 sheet: -0.57 (0.25), residues: 451 loop : -0.95 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.019 0.001 TYR A 92 PHE 0.011 0.001 PHE A 139 TRP 0.013 0.001 TRP E 430 HIS 0.017 0.001 HIS E 490 Details of bonding type rmsd covalent geometry : bond 0.00312 (11809) covalent geometry : angle 0.60771 (16078) SS BOND : bond 0.00255 ( 34) SS BOND : angle 0.88837 ( 68) hydrogen bonds : bond 0.03242 ( 299) hydrogen bonds : angle 5.79314 ( 783) link_BETA1-4 : bond 0.00610 ( 4) link_BETA1-4 : angle 2.52487 ( 12) link_NAG-ASN : bond 0.00532 ( 5) link_NAG-ASN : angle 3.21554 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.20 seconds wall clock time: 71 minutes 38.44 seconds (4298.44 seconds total)