Starting phenix.real_space_refine on Wed May 14 11:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.map" model { file = "/net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6j_18188/05_2025/8q6j_18188.cif" } resolution = 3.3 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= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7213 2.51 5 N 1969 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.86, per 1000 atoms: 0.59 Number of scatterers: 11535 At special positions: 0 Unit cell: (105.56, 129.92, 148.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2272 8.00 N 1969 7.00 C 7213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS D 216 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 170 " distance=2.03 Simple disulfide: pdb=" SG CYS E 173 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 202 " - pdb=" SG CYS E 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 222 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 233 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 246 " - pdb=" SG CYS E 273 " distance=2.03 Simple disulfide: pdb=" SG CYS E 277 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 320 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 453 " - pdb=" SG CYS E 482 " distance=2.03 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.02 Simple disulfide: pdb=" SG CYS E 493 " - pdb=" SG CYS E 506 " distance=2.02 Simple disulfide: pdb=" SG CYS E 509 " - pdb=" SG CYS E 518 " distance=2.03 Simple disulfide: pdb=" SG CYS E 522 " - pdb=" SG CYS E 538 " distance=2.03 Simple disulfide: pdb=" SG CYS E 541 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 545 " - pdb=" SG CYS E 562 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 574 " distance=2.02 Simple disulfide: pdb=" SG CYS E 578 " - pdb=" SG CYS E 601 " distance=2.03 Simple disulfide: pdb=" SG CYS E 604 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 612 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG E 701 " - " ASN E 46 " " NAG E 702 " - " ASN E 508 " " NAG E 703 " - " ASN E 549 " " NAG G 1 " - " ASN E 165 " " NAG J 1 " - " ASN E 237 " Time building additional restraints: 2.81 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 33 sheets defined 9.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.982A pdb=" N GLY A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.025A pdb=" N ASP B 31 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 32 " --> pdb=" O ILE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.872A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.443A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.777A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.777A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.699A pdb=" N GLY D 190 " --> pdb=" O SER D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'E' and resid 16 through 28 removed outlier: 4.528A pdb=" N ASP E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.531A pdb=" N LEU E 52 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.514A pdb=" N ASP E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.860A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.962A pdb=" N CYS E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 4.083A pdb=" N CYS E 230 " --> pdb=" O HIS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 374 through 378 removed outlier: 4.254A pdb=" N VAL E 377 " --> pdb=" O GLN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 486 Processing helix chain 'E' and resid 493 through 497 removed outlier: 3.656A pdb=" N GLY E 496 " --> pdb=" O CYS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.720A pdb=" N GLN E 561 " --> pdb=" O GLU E 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 5.812A pdb=" N LEU A 46 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN A 37 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.641A pdb=" N TYR A 173 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 150 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.673A pdb=" N THR B 117 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.095A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 188 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS B 171 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 6.095A pdb=" N TYR B 183 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 184 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 176 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.750A pdb=" N TYR B 201 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.602A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.586A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.509A pdb=" N TYR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 117 Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 150 removed outlier: 4.114A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.430A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.473A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.473A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AC4, first strand: chain 'E' and resid 38 through 41 removed outlier: 5.252A pdb=" N GLY E 130 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 236 through 238 Processing sheet with id=AC6, first strand: chain 'E' and resid 250 through 252 Processing sheet with id=AC7, first strand: chain 'E' and resid 267 through 269 Processing sheet with id=AC8, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 301 Processing sheet with id=AD1, first strand: chain 'E' and resid 320 through 321 removed outlier: 7.073A pdb=" N CYS E 320 " --> pdb=" O PHE E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD3, first strand: chain 'E' and resid 444 through 447 removed outlier: 3.692A pdb=" N LEU E 472 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE E 446 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR E 474 " --> pdb=" O ILE E 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 531 through 533 Processing sheet with id=AD5, first strand: chain 'E' and resid 568 through 570 Processing sheet with id=AD6, first strand: chain 'E' and resid 593 through 595 328 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 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: 3781 1.34 - 1.46: 2766 1.46 - 1.58: 5169 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11809 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C LEU E 43 " pdb=" N PRO E 44 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.25e-02 6.40e+03 4.60e+00 bond pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.36e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15791 2.38 - 4.77: 253 4.77 - 7.15: 30 7.15 - 9.54: 2 9.54 - 11.92: 2 Bond angle restraints: 16078 Sorted by residual: angle pdb=" N GLY D 97 " pdb=" CA GLY D 97 " pdb=" C GLY D 97 " ideal model delta sigma weight residual 112.34 104.64 7.70 2.04e+00 2.40e-01 1.42e+01 angle pdb=" C LEU E 423 " pdb=" N GLN E 424 " pdb=" CA GLN E 424 " ideal model delta sigma weight residual 122.37 128.82 -6.45 1.72e+00 3.38e-01 1.41e+01 angle pdb=" C VAL D 48 " pdb=" N ALA D 49 " pdb=" CA ALA D 49 " ideal model delta sigma weight residual 121.80 115.82 5.98 1.71e+00 3.42e-01 1.22e+01 angle pdb=" N THR E 422 " pdb=" CA THR E 422 " pdb=" C THR E 422 " ideal model delta sigma weight residual 110.80 103.50 7.30 2.13e+00 2.20e-01 1.17e+01 angle pdb=" CA LEU E 400 " pdb=" CB LEU E 400 " pdb=" CG LEU E 400 " ideal model delta sigma weight residual 116.30 128.22 -11.92 3.50e+00 8.16e-02 1.16e+01 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 6871 23.60 - 47.20: 317 47.20 - 70.80: 49 70.80 - 94.41: 17 94.41 - 118.01: 14 Dihedral angle restraints: 7268 sinusoidal: 2963 harmonic: 4305 Sorted by residual: dihedral pdb=" CA PHE D 99A" pdb=" C PHE D 99A" pdb=" N TYR D 99B" pdb=" CA TYR D 99B" ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE E 446 " pdb=" C ILE E 446 " pdb=" N HIS E 447 " pdb=" CA HIS E 447 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU D 96 " pdb=" C LEU D 96 " pdb=" N GLY D 97 " pdb=" CA GLY D 97 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1408 0.054 - 0.107: 358 0.107 - 0.161: 46 0.161 - 0.215: 2 0.215 - 0.269: 3 Chirality restraints: 1817 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 549 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1814 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 502 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO E 503 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 503 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 503 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 124 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LEU D 124 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU D 124 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 125 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 148 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO D 149 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 234 2.60 - 3.18: 10479 3.18 - 3.75: 17642 3.75 - 4.33: 24425 4.33 - 4.90: 39705 Nonbonded interactions: 92485 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OD1 ASN E 46 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR E 422 " pdb=" OE1 GLN E 424 " model vdw 2.064 3.040 nonbonded pdb=" O LEU E 423 " pdb=" O HIS E 447 " model vdw 2.093 3.040 nonbonded pdb=" NH2 ARG E 434 " pdb=" O THR E 504 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP D 35 " pdb=" ND2 ASN D 95 " model vdw 2.098 3.120 ... (remaining 92480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'C' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name SG )))) } ncs_group { reference = (chain 'B' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )))) selection = (chain 'D' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 11852 Z= 0.327 Angle : 0.767 11.919 16173 Z= 0.392 Chirality : 0.048 0.269 1817 Planarity : 0.006 0.059 2085 Dihedral : 15.115 118.008 4412 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.57 % Favored : 90.36 % Rotamer: Outliers : 5.69 % Allowed : 10.05 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.22), residues: 1484 helix: -1.46 (0.70), residues: 49 sheet: -0.60 (0.26), residues: 410 loop : -1.31 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 393 HIS 0.005 0.001 HIS E 447 PHE 0.020 0.002 PHE E 454 TYR 0.020 0.002 TYR E 389 ARG 0.005 0.001 ARG E 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 5) link_NAG-ASN : angle 3.14031 ( 15) link_BETA1-4 : bond 0.00669 ( 4) link_BETA1-4 : angle 1.52020 ( 12) hydrogen bonds : bond 0.13894 ( 299) hydrogen bonds : angle 7.14729 ( 783) SS BOND : bond 0.00468 ( 34) SS BOND : angle 1.11497 ( 68) covalent geometry : bond 0.00703 (11809) covalent geometry : angle 0.75847 (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 167 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 94 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 ASP cc_start: 0.8721 (m-30) cc_final: 0.8328 (m-30) REVERT: B 178 GLN cc_start: 0.2085 (mt0) cc_final: 0.1287 (mm110) REVERT: B 206 ASN cc_start: 0.7006 (t0) cc_final: 0.6647 (m-40) REVERT: C 75 ILE cc_start: 0.7840 (mm) cc_final: 0.7052 (tt) REVERT: C 81 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7709 (mp0) REVERT: C 199 GLN cc_start: 0.9011 (pt0) cc_final: 0.8787 (pm20) REVERT: E 71 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: E 95 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7960 (pp) REVERT: E 116 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7861 (ttm-80) REVERT: E 342 PHE cc_start: 0.7664 (m-80) cc_final: 0.7339 (m-80) REVERT: E 466 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8261 (p0) outliers start: 73 outliers final: 35 residues processed: 162 average time/residue: 0.2501 time to fit residues: 56.9248 Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 51 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 212 ASP Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 512 PHE Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 147 GLN B 162 ASN B 171 HIS B 178 GLN C 37 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 37 ASN E 68 GLN E 227 HIS E 297 ASN E 416 ASN E 451 HIS E 462 GLN E 466 ASN E 511 GLN E 561 GLN E 624 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.073285 restraints weight = 45939.786| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 7.40 r_work: 0.3503 rms_B_bonded: 6.67 restraints_weight: 2.0000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11852 Z= 0.175 Angle : 0.700 10.535 16173 Z= 0.346 Chirality : 0.047 0.254 1817 Planarity : 0.005 0.078 2085 Dihedral : 12.126 102.813 1863 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 3.66 % Allowed : 14.03 % Favored : 82.31 % 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: -1.47 (0.22), residues: 1484 helix: -1.73 (0.62), residues: 52 sheet: -0.77 (0.24), residues: 432 loop : -1.04 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 393 HIS 0.005 0.001 HIS B 35 PHE 0.026 0.002 PHE D 122 TYR 0.012 0.002 TYR D 145 ARG 0.008 0.001 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 5) link_NAG-ASN : angle 2.94716 ( 15) link_BETA1-4 : bond 0.00888 ( 4) link_BETA1-4 : angle 2.66072 ( 12) hydrogen bonds : bond 0.03828 ( 299) hydrogen bonds : angle 6.22432 ( 783) SS BOND : bond 0.00304 ( 34) SS BOND : angle 1.03867 ( 68) covalent geometry : bond 0.00386 (11809) covalent geometry : angle 0.68921 (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 105 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 58 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8312 (ptm160) REVERT: C 75 ILE cc_start: 0.7753 (mm) cc_final: 0.7263 (tt) REVERT: C 81 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7606 (mp0) REVERT: C 148 TRP cc_start: 0.5666 (m100) cc_final: 0.5436 (m100) REVERT: C 179 LEU cc_start: 0.8438 (tp) cc_final: 0.8222 (tp) REVERT: C 199 GLN cc_start: 0.9053 (pt0) cc_final: 0.8810 (pm20) REVERT: E 71 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7960 (pp30) REVERT: E 95 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8026 (pp) REVERT: E 116 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7729 (ttm-80) REVERT: E 342 PHE cc_start: 0.7434 (m-80) cc_final: 0.7076 (m-80) REVERT: E 455 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7119 (p) REVERT: E 465 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8230 (mmt-90) REVERT: E 466 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8452 (p0) REVERT: E 519 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6973 (p) outliers start: 47 outliers final: 25 residues processed: 101 average time/residue: 0.2322 time to fit residues: 34.8685 Evaluate side-chains 81 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 48 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 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: 0.0030 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN E 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.105350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.073409 restraints weight = 46261.261| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 6.92 r_work: 0.3517 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11852 Z= 0.153 Angle : 0.644 10.638 16173 Z= 0.316 Chirality : 0.046 0.261 1817 Planarity : 0.005 0.074 2085 Dihedral : 10.768 99.421 1841 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 3.98 % Allowed : 15.51 % Favored : 80.51 % 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: -1.38 (0.66), residues: 46 sheet: -0.48 (0.25), residues: 410 loop : -1.02 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 430 HIS 0.005 0.001 HIS B 35 PHE 0.014 0.001 PHE E 512 TYR 0.013 0.001 TYR A 92 ARG 0.007 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 5) link_NAG-ASN : angle 2.96352 ( 15) link_BETA1-4 : bond 0.00722 ( 4) link_BETA1-4 : angle 2.44730 ( 12) hydrogen bonds : bond 0.03636 ( 299) hydrogen bonds : angle 6.01537 ( 783) SS BOND : bond 0.00400 ( 34) SS BOND : angle 0.97085 ( 68) covalent geometry : bond 0.00340 (11809) covalent geometry : angle 0.63321 (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 103 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 52 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8279 (ptm160) REVERT: C 14 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8462 (m) REVERT: C 81 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7657 (mp0) REVERT: C 134 CYS cc_start: 0.6194 (t) cc_final: 0.5934 (t) REVERT: C 148 TRP cc_start: 0.5726 (m100) cc_final: 0.4536 (m100) REVERT: C 179 LEU cc_start: 0.8475 (tp) cc_final: 0.8224 (mt) REVERT: C 199 GLN cc_start: 0.9037 (pt0) cc_final: 0.8786 (pm20) REVERT: D 83 ARG cc_start: 0.8318 (mtm110) cc_final: 0.7958 (mtm180) REVERT: E 71 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7935 (pp30) REVERT: E 95 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (pp) REVERT: E 116 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7641 (ttm-80) REVERT: E 342 PHE cc_start: 0.7347 (m-80) cc_final: 0.6995 (m-80) REVERT: E 409 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 455 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.7081 (p) REVERT: E 465 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8202 (mmt-90) REVERT: E 466 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8479 (p0) outliers start: 51 outliers final: 32 residues processed: 98 average time/residue: 0.2339 time to fit residues: 33.4205 Evaluate side-chains 88 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 47 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 533 VAL 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: 7.9990 chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 0.0170 chunk 48 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.105621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.074039 restraints weight = 45845.985| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 7.01 r_work: 0.3520 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11852 Z= 0.143 Angle : 0.626 10.991 16173 Z= 0.306 Chirality : 0.045 0.260 1817 Planarity : 0.005 0.067 2085 Dihedral : 9.858 93.794 1833 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.86 % Rotamer: Outliers : 3.82 % Allowed : 16.76 % Favored : 79.42 % 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: -1.44 (0.67), residues: 47 sheet: -0.49 (0.25), residues: 428 loop : -0.94 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 430 HIS 0.004 0.001 HIS B 35 PHE 0.015 0.001 PHE A 139 TYR 0.013 0.001 TYR A 92 ARG 0.004 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 5) link_NAG-ASN : angle 2.95630 ( 15) link_BETA1-4 : bond 0.00700 ( 4) link_BETA1-4 : angle 2.38825 ( 12) hydrogen bonds : bond 0.03399 ( 299) hydrogen bonds : angle 5.84045 ( 783) SS BOND : bond 0.00272 ( 34) SS BOND : angle 0.84390 ( 68) covalent geometry : bond 0.00317 (11809) covalent geometry : angle 0.61571 (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 99 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 50 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8480 (m) REVERT: C 81 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7674 (mp0) REVERT: C 134 CYS cc_start: 0.6448 (t) cc_final: 0.6181 (t) REVERT: C 148 TRP cc_start: 0.5597 (m100) cc_final: 0.4308 (m100) REVERT: C 179 LEU cc_start: 0.8505 (tp) cc_final: 0.8222 (mt) REVERT: E 95 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8043 (pp) REVERT: E 409 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7967 (tt) REVERT: E 455 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7019 (p) REVERT: E 465 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8200 (mmt-90) REVERT: E 466 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8571 (p0) outliers start: 49 outliers final: 34 residues processed: 94 average time/residue: 0.2215 time to fit residues: 31.6704 Evaluate side-chains 85 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 45 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.103577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.071582 restraints weight = 46068.191| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 6.53 r_work: 0.3455 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11852 Z= 0.266 Angle : 0.715 11.701 16173 Z= 0.355 Chirality : 0.047 0.262 1817 Planarity : 0.005 0.072 2085 Dihedral : 9.634 89.104 1825 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.30 % Favored : 90.63 % Rotamer: Outliers : 4.91 % Allowed : 16.99 % Favored : 78.10 % 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: -1.49 (0.22), residues: 1484 helix: -1.73 (0.64), residues: 52 sheet: -0.54 (0.26), residues: 407 loop : -1.18 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 393 HIS 0.005 0.001 HIS E 235 PHE 0.020 0.002 PHE E 454 TYR 0.019 0.002 TYR E 389 ARG 0.004 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 5) link_NAG-ASN : angle 3.08267 ( 15) link_BETA1-4 : bond 0.00848 ( 4) link_BETA1-4 : angle 2.34032 ( 12) hydrogen bonds : bond 0.04027 ( 299) hydrogen bonds : angle 6.11894 ( 783) SS BOND : bond 0.00366 ( 34) SS BOND : angle 1.08216 ( 68) covalent geometry : bond 0.00588 (11809) covalent geometry : angle 0.70408 (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 110 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 47 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7774 (mmm) cc_final: 0.6252 (mmm) REVERT: B 98 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8313 (ptm160) REVERT: C 81 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7692 (mp0) REVERT: C 148 TRP cc_start: 0.5778 (m100) cc_final: 0.4665 (m100) REVERT: C 179 LEU cc_start: 0.8477 (tp) cc_final: 0.8207 (mt) REVERT: C 194 CYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5399 (p) REVERT: E 71 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8090 (pp30) REVERT: E 95 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8259 (pp) REVERT: E 116 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: E 409 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7995 (tt) REVERT: E 466 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8688 (p0) outliers start: 63 outliers final: 43 residues processed: 106 average time/residue: 0.2125 time to fit residues: 33.8379 Evaluate side-chains 94 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 44 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 533 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: 2.9990 chunk 131 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 139 optimal weight: 0.0980 chunk 15 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.106076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.074626 restraints weight = 46254.593| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 6.86 r_work: 0.3539 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11852 Z= 0.109 Angle : 0.620 11.991 16173 Z= 0.303 Chirality : 0.044 0.252 1817 Planarity : 0.005 0.060 2085 Dihedral : 8.701 76.932 1825 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 3.51 % Allowed : 18.86 % Favored : 77.63 % 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: -1.27 (0.22), residues: 1484 helix: -2.03 (0.60), residues: 53 sheet: -0.52 (0.25), residues: 426 loop : -0.93 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 430 HIS 0.005 0.001 HIS E 327 PHE 0.016 0.001 PHE A 139 TYR 0.015 0.001 TYR A 92 ARG 0.002 0.000 ARG B 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 5) link_NAG-ASN : angle 3.04123 ( 15) link_BETA1-4 : bond 0.00579 ( 4) link_BETA1-4 : angle 2.41947 ( 12) hydrogen bonds : bond 0.03150 ( 299) hydrogen bonds : angle 5.83765 ( 783) SS BOND : bond 0.00365 ( 34) SS BOND : angle 0.81435 ( 68) covalent geometry : bond 0.00248 (11809) covalent geometry : angle 0.60898 (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 95 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 50 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7554 (mmm) cc_final: 0.6371 (mmm) REVERT: B 98 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8269 (ptm160) REVERT: C 81 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7714 (mp0) REVERT: C 125 LEU cc_start: 0.7318 (mt) cc_final: 0.6928 (mt) REVERT: C 148 TRP cc_start: 0.5798 (m100) cc_final: 0.4599 (m100) REVERT: C 179 LEU cc_start: 0.8469 (tp) cc_final: 0.8190 (mt) REVERT: E 71 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7939 (pp30) REVERT: E 95 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8239 (pp) REVERT: E 409 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (tt) REVERT: E 466 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8748 (p0) outliers start: 45 outliers final: 30 residues processed: 89 average time/residue: 0.2285 time to fit residues: 30.9470 Evaluate side-chains 81 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 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: 0.5980 chunk 117 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.103887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.072561 restraints weight = 47046.652| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 6.04 r_work: 0.3527 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11852 Z= 0.231 Angle : 0.689 11.511 16173 Z= 0.340 Chirality : 0.046 0.261 1817 Planarity : 0.005 0.063 2085 Dihedral : 8.013 59.861 1818 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.51 % Rotamer: Outliers : 4.44 % Allowed : 18.78 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.39 (0.22), residues: 1484 helix: -2.09 (0.61), residues: 53 sheet: -0.40 (0.26), residues: 395 loop : -1.11 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 393 HIS 0.006 0.001 HIS B 35 PHE 0.018 0.002 PHE E 454 TYR 0.019 0.002 TYR E 387 ARG 0.005 0.000 ARG E 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 5) link_NAG-ASN : angle 3.49277 ( 15) link_BETA1-4 : bond 0.00633 ( 4) link_BETA1-4 : angle 2.62067 ( 12) hydrogen bonds : bond 0.03795 ( 299) hydrogen bonds : angle 5.99548 ( 783) SS BOND : bond 0.00349 ( 34) SS BOND : angle 1.54043 ( 68) covalent geometry : bond 0.00510 (11809) covalent geometry : angle 0.67184 (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 102 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 45 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8385 (ptm160) REVERT: C 81 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7696 (mp0) REVERT: C 125 LEU cc_start: 0.7377 (mt) cc_final: 0.6923 (mt) REVERT: C 148 TRP cc_start: 0.6539 (m100) cc_final: 0.4168 (m100) REVERT: C 179 LEU cc_start: 0.8540 (tp) cc_final: 0.8242 (mt) REVERT: E 71 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8212 (pp30) REVERT: E 95 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8602 (pp) REVERT: E 116 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8198 (ttm-80) REVERT: E 409 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8189 (tt) outliers start: 57 outliers final: 42 residues processed: 96 average time/residue: 0.2129 time to fit residues: 31.0206 Evaluate side-chains 91 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 44 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 0.0170 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.104825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.073673 restraints weight = 46438.282| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 6.18 r_work: 0.3554 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11852 Z= 0.160 Angle : 0.643 10.002 16173 Z= 0.318 Chirality : 0.045 0.253 1817 Planarity : 0.005 0.061 2085 Dihedral : 7.422 59.770 1816 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 4.29 % Allowed : 19.10 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.32 (0.22), residues: 1484 helix: -2.02 (0.62), residues: 53 sheet: -0.40 (0.26), residues: 400 loop : -1.04 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 430 HIS 0.005 0.001 HIS B 35 PHE 0.014 0.002 PHE A 139 TYR 0.017 0.002 TYR A 92 ARG 0.004 0.000 ARG E 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 5) link_NAG-ASN : angle 3.59470 ( 15) link_BETA1-4 : bond 0.00688 ( 4) link_BETA1-4 : angle 2.39729 ( 12) hydrogen bonds : bond 0.03473 ( 299) hydrogen bonds : angle 5.92021 ( 783) SS BOND : bond 0.00362 ( 34) SS BOND : angle 1.13576 ( 68) covalent geometry : bond 0.00358 (11809) covalent geometry : angle 0.62731 (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 100 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 45 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7573 (mmm) cc_final: 0.6250 (mmm) REVERT: B 87 ARG cc_start: 0.7320 (mpt-90) cc_final: 0.6912 (ptp90) REVERT: C 81 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7727 (mp0) REVERT: C 148 TRP cc_start: 0.5945 (m100) cc_final: 0.4762 (m100) REVERT: C 179 LEU cc_start: 0.8571 (tp) cc_final: 0.8229 (mt) REVERT: E 71 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8166 (pp30) REVERT: E 95 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 409 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8131 (tt) outliers start: 55 outliers final: 45 residues processed: 94 average time/residue: 0.2133 time to fit residues: 30.4112 Evaluate side-chains 91 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 43 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 477 ARG Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 8 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.102793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.071872 restraints weight = 46915.260| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 5.49 r_work: 0.3503 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11852 Z= 0.287 Angle : 0.745 10.293 16173 Z= 0.374 Chirality : 0.047 0.258 1817 Planarity : 0.005 0.069 2085 Dihedral : 7.613 59.539 1816 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.64 % Favored : 90.30 % Rotamer: Outliers : 4.68 % Allowed : 19.02 % Favored : 76.31 % 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: -1.60 (0.22), residues: 1484 helix: -2.34 (0.55), residues: 59 sheet: -0.43 (0.26), residues: 395 loop : -1.30 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 393 HIS 0.016 0.002 HIS E 490 PHE 0.020 0.002 PHE E 454 TYR 0.032 0.002 TYR A 92 ARG 0.010 0.001 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 5) link_NAG-ASN : angle 3.64887 ( 15) link_BETA1-4 : bond 0.00606 ( 4) link_BETA1-4 : angle 2.52734 ( 12) hydrogen bonds : bond 0.04130 ( 299) hydrogen bonds : angle 6.24564 ( 783) SS BOND : bond 0.00412 ( 34) SS BOND : angle 1.31862 ( 68) covalent geometry : bond 0.00634 (11809) covalent geometry : angle 0.73015 (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 101 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 41 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7714 (mmm) cc_final: 0.6274 (mmm) REVERT: C 38 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 81 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7711 (mp0) REVERT: C 148 TRP cc_start: 0.6233 (m100) cc_final: 0.5128 (m100) REVERT: C 179 LEU cc_start: 0.8595 (tp) cc_final: 0.8278 (mt) REVERT: E 71 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8381 (pp30) REVERT: E 95 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8554 (pp) outliers start: 60 outliers final: 49 residues processed: 95 average time/residue: 0.1974 time to fit residues: 29.1552 Evaluate side-chains 93 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 41 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.104612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.073527 restraints weight = 46530.487| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 6.06 r_work: 0.3550 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11852 Z= 0.154 Angle : 0.645 9.527 16173 Z= 0.322 Chirality : 0.045 0.251 1817 Planarity : 0.005 0.064 2085 Dihedral : 7.266 59.757 1816 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 3.74 % Allowed : 19.95 % Favored : 76.31 % 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: -1.44 (0.22), residues: 1484 helix: -2.28 (0.56), residues: 59 sheet: -0.49 (0.26), residues: 404 loop : -1.10 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 430 HIS 0.013 0.001 HIS E 490 PHE 0.013 0.002 PHE A 139 TYR 0.027 0.002 TYR A 92 ARG 0.007 0.000 ARG E 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 5) link_NAG-ASN : angle 3.28815 ( 15) link_BETA1-4 : bond 0.00609 ( 4) link_BETA1-4 : angle 2.56026 ( 12) hydrogen bonds : bond 0.03511 ( 299) hydrogen bonds : angle 6.03030 ( 783) SS BOND : bond 0.00299 ( 34) SS BOND : angle 1.08234 ( 68) covalent geometry : bond 0.00344 (11809) covalent geometry : angle 0.63147 (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 93 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 45 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7573 (mmm) cc_final: 0.6338 (mmm) REVERT: C 148 TRP cc_start: 0.6183 (m100) cc_final: 0.5025 (m100) REVERT: C 179 LEU cc_start: 0.8630 (tp) cc_final: 0.8275 (mt) REVERT: E 71 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (pp30) REVERT: E 95 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8594 (pp) REVERT: E 409 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8096 (tt) outliers start: 48 outliers final: 44 residues processed: 87 average time/residue: 0.1990 time to fit residues: 27.0154 Evaluate side-chains 89 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 42 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 490 HIS Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.104839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.073749 restraints weight = 46670.470| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 6.45 r_work: 0.3561 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11852 Z= 0.147 Angle : 0.630 9.528 16173 Z= 0.314 Chirality : 0.045 0.256 1817 Planarity : 0.005 0.059 2085 Dihedral : 7.049 59.904 1816 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 4.21 % Allowed : 19.88 % Favored : 75.92 % 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: -1.41 (0.22), residues: 1484 helix: -2.20 (0.57), residues: 59 sheet: -0.65 (0.25), residues: 423 loop : -0.99 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 393 HIS 0.012 0.001 HIS E 490 PHE 0.014 0.001 PHE A 139 TYR 0.029 0.002 TYR A 92 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 5) link_NAG-ASN : angle 3.25355 ( 15) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 2.53478 ( 12) hydrogen bonds : bond 0.03349 ( 299) hydrogen bonds : angle 5.86972 ( 783) SS BOND : bond 0.00290 ( 34) SS BOND : angle 1.03513 ( 68) covalent geometry : bond 0.00331 (11809) covalent geometry : angle 0.61653 (16078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8833.75 seconds wall clock time: 152 minutes 42.02 seconds (9162.02 seconds total)