Starting phenix.real_space_refine on Sat Aug 23 10:52:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.map" model { file = "/net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pwh_17993/08_2025/8pwh_17993.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 1.172 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 8 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: 2.27, per 1000 atoms: 0.20 Number of scatterers: 11535 At special positions: 0 Unit cell: (105.56, 131.08, 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=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 493 " - pdb=" SG CYS E 506 " distance=2.03 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=2.03 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: 1.07 Conformation dependent library (CDL) restraints added in 597.4 milliseconds Enol-peptide restraints added in 476.8 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 32 sheets defined 9.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.969A pdb=" N GLY A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.636A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP B 31 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.892A 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 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: 3.849A 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: 4.201A 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: 3.769A 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: 3.830A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.252A pdb=" N ASP E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.569A pdb=" N LEU E 52 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.548A 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: 3.982A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 4.024A pdb=" N CYS E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 removed outlier: 4.005A pdb=" N CYS E 213 " --> pdb=" O PRO E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 4.062A pdb=" N CYS E 230 " --> pdb=" O HIS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.592A pdb=" N ALA E 343 " --> pdb=" O GLN E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 371 through 378 removed outlier: 4.184A pdb=" N LEU E 375 " --> pdb=" O PRO E 372 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN E 376 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 4.287A 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: 3.639A pdb=" N GLY E 496 " --> pdb=" O CYS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.549A 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: 6.624A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.921A 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: 3.781A pdb=" N THR B 117 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.198A 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: 5.933A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 188 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 5.933A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 184 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.906A 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: 3.772A 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: 4.066A pdb=" N THR C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.252A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.718A 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: 3.915A 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 removed outlier: 3.580A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 72 " --> pdb=" O THR D 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.562A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 101 " --> pdb=" O ARG D 94 " (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: 5.572A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.102A 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: 5.572A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.102A 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: 5.123A 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: 7.005A pdb=" N CYS E 320 " --> pdb=" O PHE E 349 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 419 through 421 removed outlier: 6.887A pdb=" N LEU E 445 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA E 444 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR E 474 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE E 446 " --> pdb=" O THR E 474 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 531 through 533 Processing sheet with id=AD4, first strand: chain 'E' and resid 568 through 570 Processing sheet with id=AD5, first strand: chain 'E' and resid 593 through 595 337 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.37 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: 3780 1.34 - 1.46: 2731 1.46 - 1.58: 5205 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 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.00e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15684 1.74 - 3.47: 337 3.47 - 5.21: 45 5.21 - 6.95: 10 6.95 - 8.69: 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 112.34 104.81 7.53 2.04e+00 2.40e-01 1.36e+01 angle pdb=" C LEU E 423 " pdb=" N GLN E 424 " pdb=" CA GLN E 424 " ideal model delta sigma weight residual 122.73 127.74 -5.01 1.62e+00 3.81e-01 9.55e+00 angle pdb=" C VAL D 48 " pdb=" N ALA D 49 " pdb=" CA ALA D 49 " ideal model delta sigma weight residual 121.80 116.93 4.87 1.71e+00 3.42e-01 8.10e+00 angle pdb=" N ILE B 29 " pdb=" CA ILE B 29 " pdb=" C ILE B 29 " ideal model delta sigma weight residual 112.98 109.67 3.31 1.25e+00 6.40e-01 7.01e+00 angle pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.60e+00 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.57: 6907 23.57 - 47.14: 281 47.14 - 70.70: 50 70.70 - 94.27: 16 94.27 - 117.84: 14 Dihedral angle restraints: 7268 sinusoidal: 2963 harmonic: 4305 Sorted by residual: 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 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 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 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C1 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O5 NAG G 1 " pdb=" C4 NAG G 1 " ideal model delta sinusoidal sigma weight residual -64.11 53.73 -117.84 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1483 0.057 - 0.114: 300 0.114 - 0.171: 30 0.171 - 0.229: 1 0.229 - 0.286: 3 Chirality restraints: 1817 Sorted by residual: 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 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 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 -2.55 0.27 2.00e-01 2.50e+01 1.88e+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 1.77e+00 ... (remaining 1814 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 124 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C LEU D 124 " -0.040 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 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO D 149 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " -0.028 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 95 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " -0.021 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 254 2.65 - 3.21: 10787 3.21 - 3.77: 17438 3.77 - 4.34: 23751 4.34 - 4.90: 38509 Nonbonded interactions: 90739 Sorted by model distance: nonbonded pdb=" O LEU E 423 " pdb=" O HIS E 447 " model vdw 2.087 3.040 nonbonded pdb=" OD1 ASP A 82 " pdb=" OH TYR A 86 " model vdw 2.109 3.040 nonbonded pdb=" O LYS A 190 " pdb=" N ARG A 211 " model vdw 2.129 3.120 nonbonded pdb=" OG1 THR E 19 " pdb=" OG1 THR E 474 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR E 7 " pdb=" OE1 GLU E 39 " model vdw 2.179 3.040 ... (remaining 90734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'C' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name SG )))) } ncs_group { reference = (chain 'B' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )))) selection = (chain 'D' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.820 Find NCS groups from input model: 0.150 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.004 0.084 11852 Z= 0.206 Angle : 0.650 9.251 16173 Z= 0.332 Chirality : 0.046 0.286 1817 Planarity : 0.005 0.047 2085 Dihedral : 14.685 117.837 4412 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.39 % Rotamer: Outliers : 4.29 % Allowed : 9.43 % Favored : 86.28 % 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: -1.53 (0.22), residues: 1484 helix: -1.67 (0.67), residues: 52 sheet: -0.53 (0.25), residues: 434 loop : -1.25 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 514 TYR 0.018 0.002 TYR D 99B PHE 0.012 0.002 PHE E 342 TRP 0.012 0.001 TRP E 393 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00445 (11809) covalent geometry : angle 0.64110 (16078) SS BOND : bond 0.00268 ( 34) SS BOND : angle 0.93529 ( 68) hydrogen bonds : bond 0.14587 ( 308) hydrogen bonds : angle 7.30810 ( 807) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 1.39710 ( 12) link_NAG-ASN : bond 0.00566 ( 5) link_NAG-ASN : angle 3.10483 ( 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 196 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.470 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: A 4 MET cc_start: 0.8561 (mmm) cc_final: 0.8002 (mmm) REVERT: A 82 ASP cc_start: 0.7861 (t0) cc_final: 0.7447 (m-30) REVERT: A 189 HIS cc_start: 0.6237 (m-70) cc_final: 0.5863 (m-70) REVERT: B 30 LYS cc_start: 0.8818 (mttt) cc_final: 0.8495 (mtpp) REVERT: B 57 TYR cc_start: 0.8002 (m-10) cc_final: 0.7709 (m-80) REVERT: C 58 VAL cc_start: 0.8190 (t) cc_final: 0.7974 (p) REVERT: C 81 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 90 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7513 (pp30) REVERT: C 138 ASN cc_start: 0.8276 (m-40) cc_final: 0.7949 (m-40) REVERT: C 195 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 138 LEU cc_start: 0.9036 (pp) cc_final: 0.8836 (pp) REVERT: D 195 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7548 (pt) REVERT: E 9 MET cc_start: 0.7165 (ptp) cc_final: 0.6836 (ptp) REVERT: E 260 MET cc_start: 0.8117 (mmt) cc_final: 0.7809 (mmt) REVERT: E 465 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8150 (mmt180) REVERT: E 593 LYS cc_start: 0.6869 (mttt) cc_final: 0.6360 (mmtp) outliers start: 55 outliers final: 28 residues processed: 189 average time/residue: 0.1277 time to fit residues: 33.0495 Evaluate side-chains 122 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU 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 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER 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 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Chi-restraints excluded: chain E residue 589 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 38 GLN C 90 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 32 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 68 GLN E 217 GLN E 227 HIS E 416 ASN E 451 HIS E 462 GLN E 526 GLN E 537 HIS E 624 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.117313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.091213 restraints weight = 33088.836| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 4.43 r_work: 0.3551 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11852 Z= 0.181 Angle : 0.680 9.586 16173 Z= 0.340 Chirality : 0.047 0.278 1817 Planarity : 0.005 0.048 2085 Dihedral : 12.314 101.312 1856 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer: Outliers : 3.66 % Allowed : 12.16 % Favored : 84.18 % 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: -1.37 (0.22), residues: 1484 helix: -1.40 (0.66), residues: 52 sheet: -0.41 (0.25), residues: 437 loop : -1.15 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 577 TYR 0.018 0.002 TYR C 49 PHE 0.014 0.002 PHE A 139 TRP 0.022 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00406 (11809) covalent geometry : angle 0.66845 (16078) SS BOND : bond 0.00474 ( 34) SS BOND : angle 1.16607 ( 68) hydrogen bonds : bond 0.04250 ( 308) hydrogen bonds : angle 6.38115 ( 807) link_BETA1-4 : bond 0.00777 ( 4) link_BETA1-4 : angle 2.52274 ( 12) link_NAG-ASN : bond 0.00544 ( 5) link_NAG-ASN : angle 3.01248 ( 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 163 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.293 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: A 4 MET cc_start: 0.8347 (mmm) cc_final: 0.7678 (mmm) REVERT: A 92 TYR cc_start: 0.8546 (t80) cc_final: 0.8019 (m-80) REVERT: A 148 TRP cc_start: 0.5153 (m100) cc_final: 0.4843 (m100) REVERT: A 189 HIS cc_start: 0.6471 (m-70) cc_final: 0.6071 (m-70) REVERT: B 3 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6856 (mp10) REVERT: B 30 LYS cc_start: 0.8967 (mttt) cc_final: 0.8699 (mtpp) REVERT: B 57 TYR cc_start: 0.8432 (m-10) cc_final: 0.8160 (m-80) REVERT: C 58 VAL cc_start: 0.8264 (t) cc_final: 0.7990 (p) REVERT: C 81 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7922 (mp0) REVERT: C 138 ASN cc_start: 0.8398 (m-40) cc_final: 0.8095 (m-40) REVERT: D 35 ASP cc_start: 0.7691 (m-30) cc_final: 0.7388 (m-30) REVERT: D 171 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7294 (mp10) REVERT: D 210 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8300 (tppt) REVERT: E 260 MET cc_start: 0.8283 (mmt) cc_final: 0.8017 (mmt) REVERT: E 465 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8353 (mmt-90) REVERT: E 466 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8211 (p0) REVERT: E 519 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8079 (p) REVERT: E 570 ASP cc_start: 0.8617 (p0) cc_final: 0.8371 (t70) outliers start: 47 outliers final: 30 residues processed: 155 average time/residue: 0.1043 time to fit residues: 23.0412 Evaluate side-chains 134 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 LEU 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 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 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 493 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 0.0030 chunk 87 optimal weight: 0.4980 chunk 105 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.0010 chunk 10 optimal weight: 0.0270 chunk 86 optimal weight: 0.0470 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.094826 restraints weight = 32762.572| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 4.52 r_work: 0.3599 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11852 Z= 0.105 Angle : 0.629 10.599 16173 Z= 0.306 Chirality : 0.046 0.283 1817 Planarity : 0.005 0.045 2085 Dihedral : 10.223 92.565 1841 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 3.12 % Allowed : 13.09 % Favored : 83.79 % 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: -1.16 (0.22), residues: 1484 helix: -1.85 (0.64), residues: 56 sheet: -0.23 (0.25), residues: 447 loop : -0.98 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.019 0.001 TYR A 186 PHE 0.023 0.001 PHE D 122 TRP 0.020 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00232 (11809) covalent geometry : angle 0.61833 (16078) SS BOND : bond 0.00366 ( 34) SS BOND : angle 0.93415 ( 68) hydrogen bonds : bond 0.03246 ( 308) hydrogen bonds : angle 5.93480 ( 807) link_BETA1-4 : bond 0.00734 ( 4) link_BETA1-4 : angle 2.39497 ( 12) link_NAG-ASN : bond 0.00609 ( 5) link_NAG-ASN : angle 2.95503 ( 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 164 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8823 (mm) cc_final: 0.8563 (mm) REVERT: A 4 MET cc_start: 0.8312 (mmm) cc_final: 0.8100 (mmm) REVERT: A 189 HIS cc_start: 0.6272 (m-70) cc_final: 0.5892 (m-70) REVERT: B 30 LYS cc_start: 0.8918 (mttt) cc_final: 0.8617 (mtpp) REVERT: B 155 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6827 (mp0) REVERT: B 161 TRP cc_start: 0.4735 (m100) cc_final: 0.4441 (m-10) REVERT: B 213 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7697 (tmtt) REVERT: C 18 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7273 (ttm-80) REVERT: C 75 ILE cc_start: 0.8202 (mm) cc_final: 0.7959 (mm) REVERT: C 81 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7856 (mp0) REVERT: C 138 ASN cc_start: 0.8334 (m-40) cc_final: 0.7920 (m-40) REVERT: D 82 MET cc_start: 0.8793 (ttm) cc_final: 0.8571 (ttm) REVERT: D 210 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8413 (tppt) REVERT: E 171 HIS cc_start: 0.8424 (m170) cc_final: 0.8222 (t-90) REVERT: E 260 MET cc_start: 0.8244 (mmt) cc_final: 0.7980 (mmt) REVERT: E 332 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7199 (mmm160) REVERT: E 465 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8449 (mmt-90) REVERT: E 466 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7995 (p0) REVERT: E 570 ASP cc_start: 0.8611 (p0) cc_final: 0.8260 (t70) outliers start: 40 outliers final: 25 residues processed: 158 average time/residue: 0.0989 time to fit residues: 22.2072 Evaluate side-chains 125 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 136 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 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 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 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 131 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.119569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.093996 restraints weight = 32907.447| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.49 r_work: 0.3600 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11852 Z= 0.124 Angle : 0.626 11.445 16173 Z= 0.306 Chirality : 0.046 0.283 1817 Planarity : 0.005 0.043 2085 Dihedral : 9.191 83.118 1824 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 2.96 % Allowed : 14.26 % Favored : 82.77 % 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: -1.12 (0.22), residues: 1484 helix: -1.76 (0.66), residues: 56 sheet: -0.18 (0.25), residues: 440 loop : -0.97 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.013 0.001 TYR C 49 PHE 0.014 0.001 PHE D 122 TRP 0.026 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00283 (11809) covalent geometry : angle 0.61445 (16078) SS BOND : bond 0.00313 ( 34) SS BOND : angle 0.93808 ( 68) hydrogen bonds : bond 0.03279 ( 308) hydrogen bonds : angle 5.88590 ( 807) link_BETA1-4 : bond 0.00687 ( 4) link_BETA1-4 : angle 2.39301 ( 12) link_NAG-ASN : bond 0.00554 ( 5) link_NAG-ASN : angle 3.06652 ( 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 148 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8389 (mmm) cc_final: 0.8045 (mmm) REVERT: A 92 TYR cc_start: 0.8611 (t80) cc_final: 0.8069 (m-80) REVERT: A 189 HIS cc_start: 0.6412 (m-70) cc_final: 0.6114 (m-70) REVERT: B 30 LYS cc_start: 0.8964 (mttt) cc_final: 0.8691 (mtpp) REVERT: B 89 GLU cc_start: 0.8038 (pm20) cc_final: 0.7793 (pm20) REVERT: B 124 LYS cc_start: 0.8183 (mttt) cc_final: 0.7764 (tttm) REVERT: B 152 TYR cc_start: 0.6199 (p90) cc_final: 0.5252 (p90) REVERT: B 155 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7063 (mm-30) REVERT: B 213 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7702 (tmtt) REVERT: C 81 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7852 (mp0) REVERT: C 138 ASN cc_start: 0.8328 (m-40) cc_final: 0.7903 (m-40) REVERT: D 102 TYR cc_start: 0.8750 (m-80) cc_final: 0.8470 (m-80) REVERT: D 210 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8335 (mmmm) REVERT: E 260 MET cc_start: 0.8232 (mmt) cc_final: 0.7970 (mmt) REVERT: E 465 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8010 (mmt-90) REVERT: E 466 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8063 (p0) REVERT: E 570 ASP cc_start: 0.8692 (p0) cc_final: 0.8297 (t70) outliers start: 38 outliers final: 21 residues processed: 146 average time/residue: 0.0945 time to fit residues: 20.0094 Evaluate side-chains 114 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 136 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 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 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 493 CYS Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.118310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.092618 restraints weight = 33009.333| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 4.46 r_work: 0.3577 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11852 Z= 0.159 Angle : 0.646 12.035 16173 Z= 0.317 Chirality : 0.046 0.280 1817 Planarity : 0.005 0.042 2085 Dihedral : 8.414 66.375 1822 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.67 % Rotamer: Outliers : 3.20 % Allowed : 14.73 % Favored : 82.07 % 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: -1.14 (0.22), residues: 1484 helix: -1.70 (0.66), residues: 55 sheet: -0.12 (0.25), residues: 433 loop : -1.02 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 18 TYR 0.022 0.002 TYR B 80 PHE 0.016 0.002 PHE D 122 TRP 0.029 0.002 TRP A 148 HIS 0.003 0.001 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00361 (11809) covalent geometry : angle 0.63302 (16078) SS BOND : bond 0.00389 ( 34) SS BOND : angle 1.01147 ( 68) hydrogen bonds : bond 0.03479 ( 308) hydrogen bonds : angle 5.80902 ( 807) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 2.43630 ( 12) link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 3.34656 ( 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 136 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8425 (mmm) cc_final: 0.8002 (mmm) REVERT: A 92 TYR cc_start: 0.8682 (t80) cc_final: 0.8115 (m-80) REVERT: A 189 HIS cc_start: 0.6372 (m-70) cc_final: 0.5974 (m-70) REVERT: B 152 TYR cc_start: 0.6250 (p90) cc_final: 0.5483 (p90) REVERT: C 81 GLU cc_start: 0.8449 (mt-10) cc_final: 0.7847 (mp0) REVERT: C 138 ASN cc_start: 0.8338 (m-40) cc_final: 0.7930 (m-40) REVERT: D 85 GLU cc_start: 0.6895 (pp20) cc_final: 0.6439 (mp0) REVERT: D 210 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8365 (mmmm) REVERT: E 260 MET cc_start: 0.8225 (mmt) cc_final: 0.7970 (mmt) REVERT: E 465 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8422 (mmt180) REVERT: E 466 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (p0) REVERT: E 519 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8192 (p) REVERT: E 570 ASP cc_start: 0.8726 (p0) cc_final: 0.8297 (t70) outliers start: 41 outliers final: 25 residues processed: 132 average time/residue: 0.0844 time to fit residues: 16.8659 Evaluate side-chains 119 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 136 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 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 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 493 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN C 158 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.091106 restraints weight = 33097.042| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 4.48 r_work: 0.3543 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11852 Z= 0.200 Angle : 0.677 9.845 16173 Z= 0.337 Chirality : 0.046 0.278 1817 Planarity : 0.005 0.043 2085 Dihedral : 7.583 58.879 1822 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 3.04 % Allowed : 14.34 % Favored : 82.62 % 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: -1.25 (0.22), residues: 1484 helix: -1.51 (0.68), residues: 54 sheet: -0.30 (0.25), residues: 439 loop : -1.07 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.016 0.002 TYR C 49 PHE 0.016 0.002 PHE D 122 TRP 0.013 0.002 TRP A 148 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00452 (11809) covalent geometry : angle 0.65936 (16078) SS BOND : bond 0.00342 ( 34) SS BOND : angle 1.23259 ( 68) hydrogen bonds : bond 0.03810 ( 308) hydrogen bonds : angle 6.05005 ( 807) link_BETA1-4 : bond 0.00527 ( 4) link_BETA1-4 : angle 2.86268 ( 12) link_NAG-ASN : bond 0.00668 ( 5) link_NAG-ASN : angle 3.85434 ( 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 133 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8511 (mmm) cc_final: 0.7911 (mmm) REVERT: A 92 TYR cc_start: 0.8725 (t80) cc_final: 0.8173 (m-80) REVERT: A 189 HIS cc_start: 0.6497 (m-70) cc_final: 0.6097 (m-70) REVERT: B 152 TYR cc_start: 0.6285 (p90) cc_final: 0.5543 (p90) REVERT: C 81 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7881 (mp0) REVERT: C 138 ASN cc_start: 0.8367 (m-40) cc_final: 0.8100 (m-40) REVERT: D 192 GLN cc_start: 0.9226 (tp40) cc_final: 0.9015 (tp-100) REVERT: D 210 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8332 (mmmm) REVERT: E 260 MET cc_start: 0.8247 (mmt) cc_final: 0.7995 (mmt) REVERT: E 466 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8261 (p0) REVERT: E 519 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (p) outliers start: 39 outliers final: 31 residues processed: 128 average time/residue: 0.0750 time to fit residues: 14.6458 Evaluate side-chains 123 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 136 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 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 ASN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.118002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.092313 restraints weight = 33199.642| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.41 r_work: 0.3569 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11852 Z= 0.146 Angle : 0.640 9.621 16173 Z= 0.318 Chirality : 0.045 0.279 1817 Planarity : 0.005 0.050 2085 Dihedral : 7.088 59.609 1818 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.81 % Allowed : 15.12 % Favored : 82.07 % 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: -1.15 (0.22), residues: 1484 helix: -1.34 (0.72), residues: 50 sheet: -0.17 (0.25), residues: 433 loop : -1.04 (0.21), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.001 TYR B 80 PHE 0.018 0.001 PHE D 122 TRP 0.016 0.001 TRP A 148 HIS 0.003 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00332 (11809) covalent geometry : angle 0.62513 (16078) SS BOND : bond 0.00296 ( 34) SS BOND : angle 1.05162 ( 68) hydrogen bonds : bond 0.03420 ( 308) hydrogen bonds : angle 5.85994 ( 807) link_BETA1-4 : bond 0.00637 ( 4) link_BETA1-4 : angle 2.76107 ( 12) link_NAG-ASN : bond 0.00530 ( 5) link_NAG-ASN : angle 3.37725 ( 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 131 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8864 (mm) cc_final: 0.8564 (mm) REVERT: A 4 MET cc_start: 0.8403 (mmm) cc_final: 0.7846 (mmm) REVERT: A 92 TYR cc_start: 0.8663 (t80) cc_final: 0.8148 (m-80) REVERT: A 173 TYR cc_start: 0.6880 (m-80) cc_final: 0.6136 (m-80) REVERT: A 189 HIS cc_start: 0.6383 (m-70) cc_final: 0.6063 (m-70) REVERT: B 152 TYR cc_start: 0.6189 (p90) cc_final: 0.5425 (p90) REVERT: C 81 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7866 (mp0) REVERT: C 138 ASN cc_start: 0.8363 (m-40) cc_final: 0.8080 (m-40) REVERT: D 210 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8361 (mmmm) REVERT: E 71 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7972 (pp30) REVERT: E 161 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8554 (tt) REVERT: E 171 HIS cc_start: 0.7990 (t-90) cc_final: 0.7627 (t-90) REVERT: E 260 MET cc_start: 0.8265 (mmt) cc_final: 0.8010 (mmt) REVERT: E 466 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8400 (p0) REVERT: E 519 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8229 (p) outliers start: 36 outliers final: 30 residues processed: 127 average time/residue: 0.0808 time to fit residues: 15.5466 Evaluate side-chains 124 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL 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 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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 Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.119118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.093435 restraints weight = 33090.184| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.46 r_work: 0.3589 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11852 Z= 0.118 Angle : 0.622 9.614 16173 Z= 0.308 Chirality : 0.045 0.282 1817 Planarity : 0.005 0.048 2085 Dihedral : 6.793 59.206 1818 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 3.20 % Allowed : 14.96 % Favored : 81.84 % 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: -1.10 (0.22), residues: 1484 helix: -1.23 (0.74), residues: 50 sheet: -0.19 (0.25), residues: 443 loop : -0.98 (0.21), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.021 0.001 TYR B 57 PHE 0.019 0.001 PHE D 122 TRP 0.014 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00272 (11809) covalent geometry : angle 0.60882 (16078) SS BOND : bond 0.00258 ( 34) SS BOND : angle 0.94027 ( 68) hydrogen bonds : bond 0.03129 ( 308) hydrogen bonds : angle 5.64359 ( 807) link_BETA1-4 : bond 0.00638 ( 4) link_BETA1-4 : angle 2.70684 ( 12) link_NAG-ASN : bond 0.00535 ( 5) link_NAG-ASN : angle 3.24258 ( 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 133 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8269 (mmm) cc_final: 0.7861 (mmm) REVERT: A 92 TYR cc_start: 0.8635 (t80) cc_final: 0.8242 (m-80) REVERT: A 173 TYR cc_start: 0.6819 (m-80) cc_final: 0.6047 (m-80) REVERT: A 189 HIS cc_start: 0.6369 (m-70) cc_final: 0.6068 (m-70) REVERT: B 152 TYR cc_start: 0.6127 (p90) cc_final: 0.5463 (p90) REVERT: C 4 MET cc_start: 0.5849 (ttp) cc_final: 0.5306 (ttp) REVERT: C 81 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7892 (mp0) REVERT: C 138 ASN cc_start: 0.8350 (m-40) cc_final: 0.7956 (m-40) REVERT: D 102 TYR cc_start: 0.8789 (m-80) cc_final: 0.8554 (m-80) REVERT: D 171 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7237 (mp10) REVERT: D 210 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8379 (mmmm) REVERT: E 71 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: E 95 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7446 (pp) REVERT: E 260 MET cc_start: 0.8272 (mmt) cc_final: 0.8022 (mmt) REVERT: E 466 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8454 (p0) REVERT: E 519 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8238 (p) REVERT: E 570 ASP cc_start: 0.8585 (p0) cc_final: 0.8202 (p0) outliers start: 41 outliers final: 27 residues processed: 129 average time/residue: 0.0838 time to fit residues: 16.4100 Evaluate side-chains 121 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 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 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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 Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.117545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.091790 restraints weight = 32773.253| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.44 r_work: 0.3553 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11852 Z= 0.178 Angle : 0.671 12.667 16173 Z= 0.330 Chirality : 0.046 0.280 1817 Planarity : 0.005 0.053 2085 Dihedral : 6.892 59.542 1818 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 2.81 % Allowed : 15.35 % Favored : 81.84 % 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: -1.14 (0.23), residues: 1484 helix: -1.26 (0.74), residues: 50 sheet: -0.17 (0.25), residues: 437 loop : -1.03 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.035 0.002 TYR B 183 PHE 0.019 0.002 PHE D 122 TRP 0.011 0.002 TRP E 430 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00403 (11809) covalent geometry : angle 0.65783 (16078) SS BOND : bond 0.00303 ( 34) SS BOND : angle 1.03764 ( 68) hydrogen bonds : bond 0.03533 ( 308) hydrogen bonds : angle 5.77085 ( 807) link_BETA1-4 : bond 0.00679 ( 4) link_BETA1-4 : angle 2.69225 ( 12) link_NAG-ASN : bond 0.00544 ( 5) link_NAG-ASN : angle 3.26003 ( 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 129 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8529 (mmm) cc_final: 0.7812 (mmm) REVERT: A 92 TYR cc_start: 0.8703 (t80) cc_final: 0.8198 (m-80) REVERT: A 173 TYR cc_start: 0.7019 (m-80) cc_final: 0.6238 (m-80) REVERT: A 189 HIS cc_start: 0.6426 (m-70) cc_final: 0.6033 (m90) REVERT: B 152 TYR cc_start: 0.6319 (p90) cc_final: 0.5510 (p90) REVERT: C 81 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7874 (mp0) REVERT: C 138 ASN cc_start: 0.8339 (m-40) cc_final: 0.8080 (m-40) REVERT: D 210 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8369 (mmmm) REVERT: E 71 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: E 95 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7380 (pp) REVERT: E 260 MET cc_start: 0.8251 (mmt) cc_final: 0.8007 (mmt) REVERT: E 519 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8283 (p) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.0740 time to fit residues: 14.2354 Evaluate side-chains 123 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR 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 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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 Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.118659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.092899 restraints weight = 33032.687| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.47 r_work: 0.3581 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11852 Z= 0.130 Angle : 0.650 11.726 16173 Z= 0.318 Chirality : 0.045 0.281 1817 Planarity : 0.005 0.047 2085 Dihedral : 6.772 59.727 1815 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.42 % Allowed : 15.82 % Favored : 81.76 % 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: -1.07 (0.23), residues: 1484 helix: -1.20 (0.74), residues: 50 sheet: -0.14 (0.26), residues: 440 loop : -0.98 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.023 0.001 TYR B 57 PHE 0.020 0.001 PHE A 83 TRP 0.012 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 Details of bonding type rmsd covalent geometry : bond 0.00297 (11809) covalent geometry : angle 0.63736 (16078) SS BOND : bond 0.00328 ( 34) SS BOND : angle 1.08905 ( 68) hydrogen bonds : bond 0.03205 ( 308) hydrogen bonds : angle 5.69277 ( 807) link_BETA1-4 : bond 0.00582 ( 4) link_BETA1-4 : angle 2.61687 ( 12) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 3.14194 ( 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 123 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8295 (mmm) cc_final: 0.7845 (mmm) REVERT: A 92 TYR cc_start: 0.8643 (t80) cc_final: 0.8273 (m-80) REVERT: A 173 TYR cc_start: 0.6931 (m-80) cc_final: 0.6047 (m-80) REVERT: A 189 HIS cc_start: 0.6409 (m-70) cc_final: 0.6034 (m90) REVERT: B 152 TYR cc_start: 0.6189 (p90) cc_final: 0.5465 (p90) REVERT: C 4 MET cc_start: 0.6277 (ttp) cc_final: 0.5894 (ttp) REVERT: C 81 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7890 (mp0) REVERT: C 138 ASN cc_start: 0.8352 (m-40) cc_final: 0.7982 (m-40) REVERT: E 71 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: E 95 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7458 (pp) REVERT: E 260 MET cc_start: 0.8302 (mmt) cc_final: 0.8055 (mmt) REVERT: E 519 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8282 (p) outliers start: 31 outliers final: 28 residues processed: 121 average time/residue: 0.0814 time to fit residues: 15.2264 Evaluate side-chains 122 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 19 THR 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 480 ASP Chi-restraints excluded: chain E residue 493 CYS 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 Chi-restraints excluded: chain E residue 578 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.116263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.090365 restraints weight = 33321.270| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 4.47 r_work: 0.3527 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11852 Z= 0.226 Angle : 0.708 10.966 16173 Z= 0.353 Chirality : 0.047 0.279 1817 Planarity : 0.005 0.047 2085 Dihedral : 7.020 57.109 1815 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 2.73 % Allowed : 15.67 % Favored : 81.61 % 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: -1.25 (0.22), residues: 1484 helix: -0.87 (0.78), residues: 46 sheet: -0.32 (0.25), residues: 442 loop : -1.09 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.020 0.002 TYR B 57 PHE 0.029 0.002 PHE A 83 TRP 0.011 0.002 TRP E 430 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00509 (11809) covalent geometry : angle 0.69478 (16078) SS BOND : bond 0.00335 ( 34) SS BOND : angle 1.26080 ( 68) hydrogen bonds : bond 0.03899 ( 308) hydrogen bonds : angle 5.96436 ( 807) link_BETA1-4 : bond 0.00599 ( 4) link_BETA1-4 : angle 2.58642 ( 12) link_NAG-ASN : bond 0.00577 ( 5) link_NAG-ASN : angle 3.25180 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.99 seconds wall clock time: 47 minutes 42.90 seconds (2862.90 seconds total)