Starting phenix.real_space_refine on Tue Jul 29 19:06:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pwh_17993/07_2025/8pwh_17993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pwh_17993/07_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_17993/07_2025/8pwh_17993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pwh_17993/07_2025/8pwh_17993.map" model { file = "/net/cci-nas-00/data/ceres_data/8pwh_17993/07_2025/8pwh_17993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pwh_17993/07_2025/8pwh_17993.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.17, per 1000 atoms: 0.62 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: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.80 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: 4.28 Time building geometry restraints manager: 3.30 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: 0.890 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.080 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- 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 : 15.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (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 TRP 0.012 0.001 TRP E 393 HIS 0.003 0.001 HIS A 189 PHE 0.012 0.002 PHE E 342 TYR 0.018 0.002 TYR D 99B ARG 0.004 0.000 ARG E 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 5) link_NAG-ASN : angle 3.10483 ( 15) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 1.39710 ( 12) hydrogen bonds : bond 0.14587 ( 308) hydrogen bonds : angle 7.30810 ( 807) SS BOND : bond 0.00268 ( 34) SS BOND : angle 0.93529 ( 68) covalent geometry : bond 0.00445 (11809) covalent geometry : angle 0.64110 (16078) *********************** 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 : 1.224 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: 0.2777 time to fit residues: 71.7398 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 : 1.219 ------------------------------------------------------------------------------- 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 124 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 37 GLN A 147 GLN ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 38 GLN C 90 GLN D 39 GLN E 32 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 68 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4142 r_free = 0.4142 target = 0.116145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.089937 restraints weight = 33102.751| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 4.45 r_work: 0.3511 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11852 Z= 0.239 Angle : 0.713 9.816 16173 Z= 0.360 Chirality : 0.048 0.280 1817 Planarity : 0.005 0.048 2085 Dihedral : 12.582 102.621 1856 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.85 % Rotamer: Outliers : 3.82 % Allowed : 12.55 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1484 helix: -1.39 (0.66), residues: 52 sheet: -0.52 (0.25), residues: 430 loop : -1.24 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.013 0.002 PHE A 139 TYR 0.018 0.002 TYR C 49 ARG 0.007 0.001 ARG E 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 5) link_NAG-ASN : angle 3.05577 ( 15) link_BETA1-4 : bond 0.00820 ( 4) link_BETA1-4 : angle 2.45999 ( 12) hydrogen bonds : bond 0.04616 ( 308) hydrogen bonds : angle 6.51968 ( 807) SS BOND : bond 0.00459 ( 34) SS BOND : angle 1.22517 ( 68) covalent geometry : bond 0.00534 (11809) covalent geometry : angle 0.70125 (16078) *********************** 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 160 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 1.484 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: 0.8415 (mmm) cc_final: 0.7656 (mmm) REVERT: A 92 TYR cc_start: 0.8584 (t80) cc_final: 0.8029 (m-80) REVERT: A 189 HIS cc_start: 0.6544 (m-70) cc_final: 0.6025 (m90) REVERT: B 30 LYS cc_start: 0.9007 (mttt) cc_final: 0.8785 (mtpp) REVERT: B 57 TYR cc_start: 0.8447 (m-10) cc_final: 0.8153 (m-80) REVERT: C 58 VAL cc_start: 0.8168 (t) cc_final: 0.7890 (p) REVERT: C 81 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7924 (mp0) REVERT: C 90 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7591 (pp30) REVERT: C 138 ASN cc_start: 0.8362 (m-40) cc_final: 0.8077 (m-40) REVERT: D 35 ASP cc_start: 0.7882 (m-30) cc_final: 0.7570 (m-30) REVERT: D 66 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6118 (mtm180) REVERT: D 171 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7222 (mp10) REVERT: D 210 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8321 (tppt) REVERT: E 260 MET cc_start: 0.8283 (mmt) cc_final: 0.8019 (mmt) REVERT: E 465 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8064 (mmt-90) REVERT: E 466 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8312 (p0) REVERT: E 519 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8054 (p) REVERT: E 570 ASP cc_start: 0.8645 (p0) cc_final: 0.8397 (t70) outliers start: 49 outliers final: 31 residues processed: 152 average time/residue: 0.2549 time to fit residues: 55.1636 Evaluate side-chains 127 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain B residue 128 VAL 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 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 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 80 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 chunk 18 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 166 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN E 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.119487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.093763 restraints weight = 32716.503| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.43 r_work: 0.3583 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1803 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= 0.109 Angle : 0.640 10.345 16173 Z= 0.313 Chirality : 0.047 0.282 1817 Planarity : 0.005 0.045 2085 Dihedral : 10.726 95.386 1844 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 3.35 % Allowed : 13.64 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1484 helix: -1.66 (0.65), residues: 54 sheet: -0.19 (0.25), residues: 433 loop : -1.07 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 148 HIS 0.005 0.001 HIS E 327 PHE 0.023 0.001 PHE D 122 TYR 0.020 0.001 TYR A 186 ARG 0.003 0.000 ARG E 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 5) link_NAG-ASN : angle 2.93011 ( 15) link_BETA1-4 : bond 0.00683 ( 4) link_BETA1-4 : angle 2.44372 ( 12) hydrogen bonds : bond 0.03499 ( 308) hydrogen bonds : angle 6.05819 ( 807) SS BOND : bond 0.00297 ( 34) SS BOND : angle 0.90856 ( 68) covalent geometry : bond 0.00243 (11809) covalent geometry : angle 0.62957 (16078) *********************** 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 161 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.201 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: 0.8379 (mmm) cc_final: 0.7988 (mmm) REVERT: A 92 TYR cc_start: 0.8569 (t80) cc_final: 0.8032 (m-80) REVERT: A 189 HIS cc_start: 0.6342 (m-70) cc_final: 0.6053 (m-70) REVERT: B 30 LYS cc_start: 0.8930 (mttt) cc_final: 0.8628 (mtpp) REVERT: B 213 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7765 (tmtt) REVERT: B 216 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7380 (ttpp) REVERT: C 81 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7837 (mp0) REVERT: C 138 ASN cc_start: 0.8350 (m-40) cc_final: 0.7974 (m-40) REVERT: D 82 MET cc_start: 0.8823 (ttm) cc_final: 0.8594 (ttm) REVERT: D 210 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8439 (tppt) REVERT: E 171 HIS cc_start: 0.8439 (m170) cc_final: 0.8212 (t-90) REVERT: E 260 MET cc_start: 0.8227 (mmt) cc_final: 0.7962 (mmt) REVERT: E 465 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (mmt-90) REVERT: E 466 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8024 (p0) REVERT: E 570 ASP cc_start: 0.8621 (p0) cc_final: 0.8295 (t70) REVERT: E 593 LYS cc_start: 0.5972 (mmtp) cc_final: 0.5691 (mmtt) outliers start: 43 outliers final: 28 residues processed: 155 average time/residue: 0.2422 time to fit residues: 54.0654 Evaluate side-chains 131 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR 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 91 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 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL 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 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 53 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 0.0050 chunk 24 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.116903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.090780 restraints weight = 33122.663| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.46 r_work: 0.3528 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11852 Z= 0.188 Angle : 0.666 11.079 16173 Z= 0.330 Chirality : 0.047 0.281 1817 Planarity : 0.005 0.042 2085 Dihedral : 9.873 88.081 1832 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 3.98 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.22), residues: 1484 helix: -1.56 (0.67), residues: 54 sheet: -0.33 (0.25), residues: 438 loop : -1.11 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.019 0.002 PHE D 122 TYR 0.019 0.002 TYR A 186 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 5) link_NAG-ASN : angle 3.07061 ( 15) link_BETA1-4 : bond 0.00673 ( 4) link_BETA1-4 : angle 2.40406 ( 12) hydrogen bonds : bond 0.03932 ( 308) hydrogen bonds : angle 6.12220 ( 807) SS BOND : bond 0.00375 ( 34) SS BOND : angle 1.02992 ( 68) covalent geometry : bond 0.00426 (11809) covalent geometry : angle 0.65421 (16078) *********************** 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 155 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 1.352 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: 0.8452 (mmm) cc_final: 0.7870 (mmm) REVERT: A 92 TYR cc_start: 0.8716 (t80) cc_final: 0.8159 (m-80) REVERT: A 173 TYR cc_start: 0.6796 (m-80) cc_final: 0.6056 (m-80) REVERT: A 189 HIS cc_start: 0.6576 (m-70) cc_final: 0.6286 (m-70) REVERT: B 1 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 30 LYS cc_start: 0.9002 (mttt) cc_final: 0.8714 (mtpp) REVERT: B 57 TYR cc_start: 0.8191 (m-80) cc_final: 0.7972 (m-80) REVERT: B 152 TYR cc_start: 0.6228 (p90) cc_final: 0.5550 (p90) REVERT: C 81 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7861 (mp0) REVERT: C 138 ASN cc_start: 0.8371 (m-40) cc_final: 0.8073 (m-40) REVERT: D 66 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5223 (ptm160) REVERT: D 83 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8299 (ttp-110) REVERT: D 85 GLU cc_start: 0.6992 (pp20) cc_final: 0.6674 (pp20) REVERT: D 210 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8392 (tppt) REVERT: E 260 MET cc_start: 0.8223 (mmt) cc_final: 0.7962 (mmt) REVERT: E 465 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8432 (mmt180) REVERT: E 466 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8388 (p0) REVERT: E 519 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8184 (p) REVERT: E 570 ASP cc_start: 0.8701 (p0) cc_final: 0.8285 (t70) outliers start: 51 outliers final: 36 residues processed: 146 average time/residue: 0.2453 time to fit residues: 51.3417 Evaluate side-chains 132 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 133 VAL 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 91 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU 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 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 109 THR Chi-restraints excluded: chain C residue 123 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** 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 = 0.4176 r_free = 0.4176 target = 0.118581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.092901 restraints weight = 32561.900| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 4.42 r_work: 0.3581 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11852 Z= 0.123 Angle : 0.624 11.950 16173 Z= 0.306 Chirality : 0.045 0.282 1817 Planarity : 0.005 0.042 2085 Dihedral : 9.021 73.718 1832 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 3.51 % Allowed : 15.28 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1484 helix: -1.58 (0.66), residues: 55 sheet: -0.09 (0.25), residues: 433 loop : -1.03 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.017 0.001 PHE D 122 TYR 0.018 0.001 TYR A 186 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 5) link_NAG-ASN : angle 3.15282 ( 15) link_BETA1-4 : bond 0.00644 ( 4) link_BETA1-4 : angle 2.38321 ( 12) hydrogen bonds : bond 0.03293 ( 308) hydrogen bonds : angle 5.85818 ( 807) SS BOND : bond 0.00241 ( 34) SS BOND : angle 0.93046 ( 68) covalent geometry : bond 0.00279 (11809) covalent geometry : angle 0.61222 (16078) *********************** 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 152 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 1.324 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 2 ILE cc_start: 0.8882 (mm) cc_final: 0.8582 (mm) REVERT: A 4 MET cc_start: 0.8311 (mmm) cc_final: 0.7875 (mmm) REVERT: A 92 TYR cc_start: 0.8620 (t80) cc_final: 0.8137 (m-80) REVERT: A 189 HIS cc_start: 0.6566 (m-70) cc_final: 0.6212 (m-70) REVERT: B 30 LYS cc_start: 0.8965 (mttt) cc_final: 0.8686 (mtpp) REVERT: B 152 TYR cc_start: 0.6108 (p90) cc_final: 0.5437 (p90) REVERT: B 216 LYS cc_start: 0.7805 (mmmt) cc_final: 0.7334 (ttpp) REVERT: C 81 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7860 (mp0) REVERT: C 138 ASN cc_start: 0.8365 (m-40) cc_final: 0.7971 (m-40) REVERT: D 210 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8245 (mmmm) REVERT: E 71 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7902 (pp30) REVERT: E 260 MET cc_start: 0.8275 (mmt) cc_final: 0.8020 (mmt) REVERT: E 466 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8299 (p0) REVERT: E 519 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8186 (p) REVERT: E 570 ASP cc_start: 0.8619 (p0) cc_final: 0.8308 (p0) outliers start: 45 outliers final: 33 residues processed: 145 average time/residue: 0.2464 time to fit residues: 51.6100 Evaluate side-chains 132 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU 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 203 CYS 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 6 GLU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** E 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.117840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.092005 restraints weight = 33320.481| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.43 r_work: 0.3564 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2218 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= 0.150 Angle : 0.653 11.057 16173 Z= 0.319 Chirality : 0.045 0.281 1817 Planarity : 0.005 0.042 2085 Dihedral : 7.990 59.387 1826 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.47 % Favored : 93.46 % Rotamer: Outliers : 3.66 % Allowed : 15.20 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1484 helix: -1.46 (0.68), residues: 55 sheet: -0.12 (0.25), residues: 435 loop : -1.02 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.018 0.001 PHE D 122 TYR 0.017 0.002 TYR B 57 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 5) link_NAG-ASN : angle 3.69270 ( 15) link_BETA1-4 : bond 0.00560 ( 4) link_BETA1-4 : angle 2.66741 ( 12) hydrogen bonds : bond 0.03460 ( 308) hydrogen bonds : angle 5.79325 ( 807) SS BOND : bond 0.00329 ( 34) SS BOND : angle 1.02467 ( 68) covalent geometry : bond 0.00342 (11809) covalent geometry : angle 0.63726 (16078) *********************** 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 141 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 1.319 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 2 ILE cc_start: 0.8941 (mm) cc_final: 0.8646 (mm) REVERT: A 4 MET cc_start: 0.8304 (mmm) cc_final: 0.7777 (mmm) REVERT: A 28 ASP cc_start: 0.7458 (t0) cc_final: 0.7212 (t0) REVERT: A 189 HIS cc_start: 0.6524 (m-70) cc_final: 0.6081 (m90) REVERT: B 152 TYR cc_start: 0.6105 (p90) cc_final: 0.5447 (p90) REVERT: C 81 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7889 (mp0) REVERT: C 138 ASN cc_start: 0.8383 (m-40) cc_final: 0.8080 (m-40) REVERT: D 66 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.5238 (ptm160) REVERT: D 83 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8275 (ttp-110) REVERT: D 85 GLU cc_start: 0.7003 (pp20) cc_final: 0.6640 (pp20) REVERT: D 102 TYR cc_start: 0.8817 (m-80) cc_final: 0.8573 (m-80) REVERT: D 210 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8384 (mmmm) REVERT: E 23 MET cc_start: 0.6720 (ptt) cc_final: 0.6492 (ptt) REVERT: E 35 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: E 71 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7975 (pp30) REVERT: E 161 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (tt) REVERT: E 260 MET cc_start: 0.8294 (mmt) cc_final: 0.8046 (mmt) REVERT: E 466 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8450 (p0) REVERT: E 519 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8326 (p) REVERT: E 570 ASP cc_start: 0.8590 (p0) cc_final: 0.8339 (p0) outliers start: 47 outliers final: 37 residues processed: 136 average time/residue: 0.2203 time to fit residues: 44.7491 Evaluate side-chains 134 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU 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 203 CYS Chi-restraints excluded: chain B residue 204 ASN 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 6 GLU 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 175 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 35 GLN 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 420 SER 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 133 optimal weight: 0.0980 chunk 117 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 144 optimal weight: 0.0270 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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** E 35 GLN ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.119688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.094131 restraints weight = 33176.308| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 4.46 r_work: 0.3605 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2423 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= 0.104 Angle : 0.623 9.837 16173 Z= 0.306 Chirality : 0.045 0.282 1817 Planarity : 0.005 0.043 2085 Dihedral : 7.371 58.232 1826 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 3.59 % Allowed : 15.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1484 helix: -1.50 (0.68), residues: 56 sheet: -0.10 (0.25), residues: 440 loop : -0.95 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.017 0.001 PHE D 122 TYR 0.016 0.001 TYR B 80 ARG 0.002 0.000 ARG E 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 5) link_NAG-ASN : angle 3.57402 ( 15) link_BETA1-4 : bond 0.00591 ( 4) link_BETA1-4 : angle 2.77217 ( 12) hydrogen bonds : bond 0.03051 ( 308) hydrogen bonds : angle 5.65570 ( 807) SS BOND : bond 0.00283 ( 34) SS BOND : angle 1.19002 ( 68) covalent geometry : bond 0.00237 (11809) covalent geometry : angle 0.60519 (16078) *********************** 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 147 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8370 (mmm) cc_final: 0.7932 (mmm) REVERT: A 92 TYR cc_start: 0.8683 (t80) cc_final: 0.8172 (m-80) REVERT: A 189 HIS cc_start: 0.6442 (m-70) cc_final: 0.6022 (m90) REVERT: B 30 LYS cc_start: 0.8929 (mttt) cc_final: 0.8685 (mtpp) REVERT: B 98 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8839 (ttp-170) REVERT: B 124 LYS cc_start: 0.8231 (mttt) cc_final: 0.7864 (tptt) REVERT: B 152 TYR cc_start: 0.6060 (p90) cc_final: 0.5232 (p90) REVERT: B 213 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7745 (tmtt) REVERT: C 81 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7863 (mp0) REVERT: C 138 ASN cc_start: 0.8331 (m-40) cc_final: 0.7923 (m-40) REVERT: D 66 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5135 (ptm160) REVERT: D 83 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8333 (ttp-110) REVERT: D 102 TYR cc_start: 0.8756 (m-80) cc_final: 0.8467 (m-80) REVERT: D 210 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8338 (mmmm) REVERT: E 23 MET cc_start: 0.6588 (ptt) cc_final: 0.6334 (ptt) REVERT: E 35 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: E 260 MET cc_start: 0.8211 (mmt) cc_final: 0.7955 (mmt) REVERT: E 466 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8271 (p0) REVERT: E 570 ASP cc_start: 0.8648 (p0) cc_final: 0.8365 (p0) outliers start: 46 outliers final: 34 residues processed: 140 average time/residue: 0.2470 time to fit residues: 49.8810 Evaluate side-chains 127 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ARG 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 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 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 6 GLU 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 131 THR Chi-restraints excluded: chain D residue 175 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 35 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 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 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 99 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 147 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 0.0270 chunk 86 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 ** E 561 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 = 0.4197 r_free = 0.4197 target = 0.119931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.094452 restraints weight = 32916.257| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 4.46 r_work: 0.3611 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2549 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= 0.106 Angle : 0.616 9.678 16173 Z= 0.303 Chirality : 0.045 0.284 1817 Planarity : 0.005 0.052 2085 Dihedral : 7.039 57.301 1824 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 3.04 % Allowed : 16.21 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1484 helix: -1.43 (0.69), residues: 56 sheet: -0.02 (0.26), residues: 440 loop : -0.89 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 161 HIS 0.004 0.001 HIS E 327 PHE 0.018 0.001 PHE D 122 TYR 0.020 0.001 TYR A 173 ARG 0.002 0.000 ARG E 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 5) link_NAG-ASN : angle 3.33567 ( 15) link_BETA1-4 : bond 0.00635 ( 4) link_BETA1-4 : angle 2.69959 ( 12) hydrogen bonds : bond 0.03038 ( 308) hydrogen bonds : angle 5.52975 ( 807) SS BOND : bond 0.00283 ( 34) SS BOND : angle 0.83740 ( 68) covalent geometry : bond 0.00244 (11809) covalent geometry : angle 0.60214 (16078) *********************** 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 143 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8353 (mmm) cc_final: 0.7915 (mmm) REVERT: A 92 TYR cc_start: 0.8640 (t80) cc_final: 0.8116 (m-80) REVERT: A 189 HIS cc_start: 0.6481 (m-70) cc_final: 0.6100 (m90) REVERT: B 30 LYS cc_start: 0.8914 (mttt) cc_final: 0.8668 (mtpp) REVERT: B 98 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8928 (ttp-170) REVERT: B 124 LYS cc_start: 0.8278 (mttt) cc_final: 0.7949 (tptt) REVERT: B 152 TYR cc_start: 0.6007 (p90) cc_final: 0.5243 (p90) REVERT: B 155 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7025 (mm-30) REVERT: B 213 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7732 (tmtt) REVERT: C 81 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7879 (mp0) REVERT: C 138 ASN cc_start: 0.8329 (m-40) cc_final: 0.7932 (m-40) REVERT: D 18 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7489 (tt) REVERT: D 66 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5214 (ptm160) REVERT: D 102 TYR cc_start: 0.8738 (m-80) cc_final: 0.8459 (m-80) REVERT: D 210 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8366 (mmmm) REVERT: E 95 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7444 (pp) REVERT: E 260 MET cc_start: 0.8234 (mmt) cc_final: 0.7983 (mmt) REVERT: E 466 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8288 (p0) outliers start: 39 outliers final: 32 residues processed: 137 average time/residue: 0.2343 time to fit residues: 46.5308 Evaluate side-chains 126 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ARG 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 203 CYS Chi-restraints excluded: chain B residue 204 ASN 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 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU 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 131 THR Chi-restraints excluded: chain D residue 175 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 95 LEU Chi-restraints excluded: chain E residue 97 ASN 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 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 10 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN ** E 561 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 = 0.4178 r_free = 0.4178 target = 0.118646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.092836 restraints weight = 33331.861| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 4.49 r_work: 0.3580 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2553 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= 0.140 Angle : 0.634 10.315 16173 Z= 0.313 Chirality : 0.045 0.281 1817 Planarity : 0.005 0.048 2085 Dihedral : 6.987 59.490 1822 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 3.12 % Allowed : 16.29 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1484 helix: -1.41 (0.69), residues: 56 sheet: 0.00 (0.26), residues: 439 loop : -0.95 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 148 HIS 0.004 0.001 HIS E 327 PHE 0.019 0.001 PHE D 122 TYR 0.021 0.002 TYR B 57 ARG 0.003 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 5) link_NAG-ASN : angle 3.35243 ( 15) link_BETA1-4 : bond 0.00577 ( 4) link_BETA1-4 : angle 2.67219 ( 12) hydrogen bonds : bond 0.03270 ( 308) hydrogen bonds : angle 5.52711 ( 807) SS BOND : bond 0.00326 ( 34) SS BOND : angle 1.04456 ( 68) covalent geometry : bond 0.00320 (11809) covalent geometry : angle 0.61995 (16078) *********************** 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 133 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8380 (mmm) cc_final: 0.7912 (mmm) REVERT: A 189 HIS cc_start: 0.6496 (m-70) cc_final: 0.6090 (m90) REVERT: B 152 TYR cc_start: 0.6144 (p90) cc_final: 0.5504 (p90) REVERT: B 155 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7068 (mm-30) REVERT: C 81 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7879 (mp0) REVERT: C 138 ASN cc_start: 0.8336 (m-40) cc_final: 0.7957 (m-40) REVERT: D 18 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7531 (tt) REVERT: D 66 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.4811 (ptm160) REVERT: D 83 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7937 (ttp-110) REVERT: D 85 GLU cc_start: 0.7308 (pp20) cc_final: 0.7015 (pp20) REVERT: D 102 TYR cc_start: 0.8751 (m-80) cc_final: 0.8478 (m-80) REVERT: D 210 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8398 (mmmm) REVERT: E 71 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7988 (pp30) REVERT: E 95 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7254 (pp) REVERT: E 171 HIS cc_start: 0.8000 (t-90) cc_final: 0.7623 (t-90) REVERT: E 260 MET cc_start: 0.8229 (mmt) cc_final: 0.7978 (mmt) REVERT: E 570 ASP cc_start: 0.8721 (p0) cc_final: 0.8502 (p0) outliers start: 40 outliers final: 34 residues processed: 127 average time/residue: 0.2222 time to fit residues: 42.5296 Evaluate side-chains 127 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 ARG 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 203 CYS Chi-restraints excluded: chain B residue 204 ASN 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 136 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU 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 110 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 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 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 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 127 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 GLN ** E 561 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 = 0.4170 r_free = 0.4170 target = 0.118102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092464 restraints weight = 33189.570| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 4.39 r_work: 0.3576 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2548 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= 0.150 Angle : 0.641 12.541 16173 Z= 0.317 Chirality : 0.045 0.279 1817 Planarity : 0.005 0.052 2085 Dihedral : 6.989 59.538 1820 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 3.04 % Allowed : 16.13 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1484 helix: -1.20 (0.74), residues: 50 sheet: -0.13 (0.25), residues: 445 loop : -0.93 (0.21), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 148 HIS 0.003 0.001 HIS E 327 PHE 0.020 0.001 PHE D 122 TYR 0.023 0.002 TYR B 57 ARG 0.002 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 5) link_NAG-ASN : angle 3.19746 ( 15) link_BETA1-4 : bond 0.00604 ( 4) link_BETA1-4 : angle 2.64367 ( 12) hydrogen bonds : bond 0.03334 ( 308) hydrogen bonds : angle 5.59445 ( 807) SS BOND : bond 0.00364 ( 34) SS BOND : angle 0.94451 ( 68) covalent geometry : bond 0.00343 (11809) covalent geometry : angle 0.62828 (16078) ********************** 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 130 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8381 (mmm) cc_final: 0.7900 (mmm) REVERT: A 189 HIS cc_start: 0.6505 (m-70) cc_final: 0.6104 (m90) REVERT: B 152 TYR cc_start: 0.6154 (p90) cc_final: 0.5463 (p90) REVERT: C 81 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7881 (mp0) REVERT: C 138 ASN cc_start: 0.8344 (m-40) cc_final: 0.7961 (m-40) REVERT: D 18 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7542 (tt) REVERT: D 66 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.4992 (ptm160) REVERT: D 83 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8120 (ttp-110) REVERT: D 85 GLU cc_start: 0.7227 (pp20) cc_final: 0.6982 (pp20) REVERT: D 171 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7179 (mp10) REVERT: E 71 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8023 (pp30) REVERT: E 95 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7311 (pp) REVERT: E 171 HIS cc_start: 0.7927 (t-90) cc_final: 0.7589 (t-90) REVERT: E 260 MET cc_start: 0.8249 (mmt) cc_final: 0.8000 (mmt) REVERT: E 513 LEU cc_start: 0.7575 (mm) cc_final: 0.7340 (mm) outliers start: 39 outliers final: 34 residues processed: 124 average time/residue: 0.2251 time to fit residues: 41.8381 Evaluate side-chains 126 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 98 ARG 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 203 CYS Chi-restraints excluded: chain B residue 204 ASN 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 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 LEU 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 110 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 191 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 420 SER 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 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 99 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN E 35 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN E 405 ASN ** E 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.089761 restraints weight = 33403.896| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.39 r_work: 0.3520 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11852 Z= 0.256 Angle : 0.724 9.864 16173 Z= 0.364 Chirality : 0.048 0.276 1817 Planarity : 0.005 0.050 2085 Dihedral : 7.331 57.076 1820 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 3.20 % Allowed : 16.06 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1484 helix: -1.20 (0.71), residues: 46 sheet: -0.33 (0.25), residues: 435 loop : -1.12 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.006 0.001 HIS A 189 PHE 0.021 0.002 PHE D 122 TYR 0.023 0.002 TYR A 186 ARG 0.003 0.000 ARG E 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 5) link_NAG-ASN : angle 3.37274 ( 15) link_BETA1-4 : bond 0.00576 ( 4) link_BETA1-4 : angle 2.65519 ( 12) hydrogen bonds : bond 0.04142 ( 308) hydrogen bonds : angle 5.98860 ( 807) SS BOND : bond 0.00449 ( 34) SS BOND : angle 1.22711 ( 68) covalent geometry : bond 0.00578 (11809) covalent geometry : angle 0.71028 (16078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6523.84 seconds wall clock time: 112 minutes 37.70 seconds (6757.70 seconds total)