Starting phenix.real_space_refine on Tue Jul 29 22:39:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6j_18188/07_2025/8q6j_18188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6j_18188/07_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_18188/07_2025/8q6j_18188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6j_18188/07_2025/8q6j_18188.map" model { file = "/net/cci-nas-00/data/ceres_data/8q6j_18188/07_2025/8q6j_18188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6j_18188/07_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-5711/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1650 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Chain: "C" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1657 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1665 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4794 Classifications: {'peptide': 624} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 579} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.72, per 1000 atoms: 0.84 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: 3.74 Conformation dependent library (CDL) restraints added in 3.0 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: 1.70 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: 4.63 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3781 1.34 - 1.46: 2766 1.46 - 1.58: 5169 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 11809 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C LEU E 43 " pdb=" N PRO E 44 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.25e-02 6.40e+03 4.60e+00 bond pdb=" CB ASP D 101 " pdb=" CG ASP D 101 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.36e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.00e+00 ... (remaining 11804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15791 2.38 - 4.77: 253 4.77 - 7.15: 30 7.15 - 9.54: 2 9.54 - 11.92: 2 Bond angle restraints: 16078 Sorted by residual: angle pdb=" N GLY D 97 " pdb=" CA GLY D 97 " pdb=" C GLY D 97 " ideal model delta sigma weight residual 112.34 104.64 7.70 2.04e+00 2.40e-01 1.42e+01 angle pdb=" C LEU E 423 " pdb=" N GLN E 424 " pdb=" CA GLN E 424 " ideal model delta sigma weight residual 122.37 128.82 -6.45 1.72e+00 3.38e-01 1.41e+01 angle pdb=" C VAL D 48 " pdb=" N ALA D 49 " pdb=" CA ALA D 49 " ideal model delta sigma weight residual 121.80 115.82 5.98 1.71e+00 3.42e-01 1.22e+01 angle pdb=" N THR E 422 " pdb=" CA THR E 422 " pdb=" C THR E 422 " ideal model delta sigma weight residual 110.80 103.50 7.30 2.13e+00 2.20e-01 1.17e+01 angle pdb=" CA LEU E 400 " pdb=" CB LEU E 400 " pdb=" CG LEU E 400 " ideal model delta sigma weight residual 116.30 128.22 -11.92 3.50e+00 8.16e-02 1.16e+01 ... (remaining 16073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.60: 6871 23.60 - 47.20: 317 47.20 - 70.80: 49 70.80 - 94.41: 17 94.41 - 118.01: 14 Dihedral angle restraints: 7268 sinusoidal: 2963 harmonic: 4305 Sorted by residual: dihedral pdb=" CA PHE D 99A" pdb=" C PHE D 99A" pdb=" N TYR D 99B" pdb=" CA TYR D 99B" ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE E 446 " pdb=" C ILE E 446 " pdb=" N HIS E 447 " pdb=" CA HIS E 447 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU D 96 " pdb=" C LEU D 96 " pdb=" N GLY D 97 " pdb=" CA GLY D 97 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1408 0.054 - 0.107: 358 0.107 - 0.161: 46 0.161 - 0.215: 2 0.215 - 0.269: 3 Chirality restraints: 1817 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG E 703 " pdb=" ND2 ASN E 549 " pdb=" C2 NAG E 703 " pdb=" O5 NAG E 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1814 not shown) Planarity restraints: 2090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 502 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO E 503 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 503 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 503 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 124 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LEU D 124 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU D 124 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 125 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 148 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO D 149 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 2087 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 234 2.60 - 3.18: 10479 3.18 - 3.75: 17642 3.75 - 4.33: 24425 4.33 - 4.90: 39705 Nonbonded interactions: 92485 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OD1 ASN E 46 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR E 422 " pdb=" OE1 GLN E 424 " model vdw 2.064 3.040 nonbonded pdb=" O LEU E 423 " pdb=" O HIS E 447 " model vdw 2.093 3.040 nonbonded pdb=" NH2 ARG E 434 " pdb=" O THR E 504 " model vdw 2.096 3.120 nonbonded pdb=" OD1 ASP D 35 " pdb=" ND2 ASN D 95 " model vdw 2.098 3.120 ... (remaining 92480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 214)) selection = (chain 'C' and (resid 1 through 23 or resid 25 through 29 or resid 33 through 52 \ or resid 55 or resid 57 through 65 or resid 67 through 90 or resid 92 or resid \ 95 or resid 97 through 213 or (resid 214 and (name N or name CA or name C or nam \ e O or name CB or name SG )))) } ncs_group { reference = (chain 'B' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 3 or resid 56 or resid 60 or resid 65 through 69 or resid 71 or resid 73 or resi \ d 75 through 78 or resid 80 through 96 or resid 98 or resid 101 or resid 104 thr \ ough 105 or resid 108 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )))) selection = (chain 'D' and (resid 1 through 27 or resid 31 or resid 36 through 49 or resid 5 \ 2A or resid 55 or resid 59 or resid 64 through 68 or resid 70 or resid 72 or res \ id 74 through 77 or resid 79 through 92 or resid 94 or resid 97 or resid 99A thr \ ough 99B or resid 101 through 213)) } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.110 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- 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 : 1.349 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: 0.2504 time to fit residues: 57.1893 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 : 1.222 ------------------------------------------------------------------------------- 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 = 77)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073282 restraints weight = 45939.768| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 7.40 r_work: 0.3505 rms_B_bonded: 6.57 restraints_weight: 2.0000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 1.794 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: 0.8560 (OUTLIER) cc_final: 0.8304 (ptm160) REVERT: C 75 ILE cc_start: 0.7766 (mm) cc_final: 0.7275 (tt) REVERT: C 81 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7606 (mp0) REVERT: C 148 TRP cc_start: 0.5632 (m100) cc_final: 0.5407 (m100) REVERT: C 179 LEU cc_start: 0.8427 (tp) cc_final: 0.8211 (tp) REVERT: C 199 GLN cc_start: 0.9051 (pt0) cc_final: 0.8811 (pm20) REVERT: E 71 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7968 (pp30) REVERT: E 95 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8019 (pp) REVERT: E 116 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7742 (ttm-80) REVERT: E 342 PHE cc_start: 0.7428 (m-80) cc_final: 0.7073 (m-80) REVERT: E 455 VAL cc_start: 0.7358 (OUTLIER) cc_final: 0.7119 (p) REVERT: E 465 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8232 (mmt-90) REVERT: E 466 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8446 (p0) REVERT: E 519 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.6954 (p) outliers start: 47 outliers final: 25 residues processed: 101 average time/residue: 0.2901 time to fit residues: 44.2199 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 : 1.294 ------------------------------------------------------------------------------- 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: 0.0770 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5140 ------------------------------------------------------------------------------- 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** E 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.105359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.073428 restraints weight = 46270.330| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 7.07 r_work: 0.3512 rms_B_bonded: 6.55 restraints_weight: 2.0000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11852 Z= 0.152 Angle : 0.644 10.559 16173 Z= 0.316 Chirality : 0.046 0.262 1817 Planarity : 0.005 0.073 2085 Dihedral : 10.775 99.422 1841 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 3.98 % Allowed : 15.74 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1484 helix: -1.39 (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 0.008 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 5) link_NAG-ASN : angle 2.96482 ( 15) link_BETA1-4 : bond 0.00727 ( 4) link_BETA1-4 : angle 2.45193 ( 12) hydrogen bonds : bond 0.03648 ( 299) hydrogen bonds : angle 6.01563 ( 783) SS BOND : bond 0.00305 ( 34) SS BOND : angle 0.97867 ( 68) covalent geometry : bond 0.00338 (11809) covalent geometry : angle 0.63268 (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 : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (ptm160) REVERT: C 14 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8460 (m) REVERT: C 81 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7652 (mp0) REVERT: C 134 CYS cc_start: 0.6197 (t) cc_final: 0.5925 (t) REVERT: C 148 TRP cc_start: 0.5757 (m100) cc_final: 0.4571 (m100) REVERT: C 179 LEU cc_start: 0.8485 (tp) cc_final: 0.8232 (mt) REVERT: C 199 GLN cc_start: 0.9037 (pt0) cc_final: 0.8786 (pm20) REVERT: D 83 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7960 (mtm180) REVERT: E 71 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7931 (pp30) REVERT: E 95 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8036 (pp) REVERT: E 116 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7635 (ttm-80) REVERT: E 342 PHE cc_start: 0.7346 (m-80) cc_final: 0.6994 (m-80) REVERT: E 409 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 455 VAL cc_start: 0.7315 (OUTLIER) cc_final: 0.7079 (p) REVERT: E 465 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8198 (mmt-90) REVERT: E 466 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (p0) outliers start: 51 outliers final: 32 residues processed: 98 average time/residue: 0.2443 time to fit residues: 35.2472 Evaluate side-chains 86 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 45 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 chunk 48 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 ASN ** 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 = 0.4364 r_free = 0.4364 target = 0.105961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.074528 restraints weight = 45762.932| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 6.86 r_work: 0.3530 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1873 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= 0.127 Angle : 0.619 10.857 16173 Z= 0.302 Chirality : 0.045 0.259 1817 Planarity : 0.005 0.066 2085 Dihedral : 9.860 93.980 1833 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 4.05 % Allowed : 16.21 % Favored : 79.73 % 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: -1.20 (0.22), residues: 1484 helix: -1.45 (0.68), residues: 47 sheet: -0.47 (0.25), residues: 428 loop : -0.92 (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 0.016 0.001 PHE A 139 TYR 0.014 0.001 TYR A 92 ARG 0.006 0.000 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 5) link_NAG-ASN : angle 2.94811 ( 15) link_BETA1-4 : bond 0.00644 ( 4) link_BETA1-4 : angle 2.40188 ( 12) hydrogen bonds : bond 0.03320 ( 299) hydrogen bonds : angle 5.81933 ( 783) SS BOND : bond 0.00262 ( 34) SS BOND : angle 0.83162 ( 68) covalent geometry : bond 0.00283 (11809) covalent geometry : angle 0.60859 (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 103 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 51 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7559 (mmm) cc_final: 0.5910 (mmm) REVERT: C 81 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7668 (mp0) REVERT: C 134 CYS cc_start: 0.6349 (t) cc_final: 0.6097 (t) REVERT: C 148 TRP cc_start: 0.5522 (m100) cc_final: 0.4231 (m100) REVERT: C 179 LEU cc_start: 0.8479 (tp) cc_final: 0.8201 (mt) REVERT: D 66 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.2652 (ptm160) REVERT: E 95 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8052 (pp) REVERT: E 409 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7884 (tt) REVERT: E 455 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6906 (p) REVERT: E 465 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8204 (mmt-90) REVERT: E 466 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8572 (p0) outliers start: 52 outliers final: 32 residues processed: 98 average time/residue: 0.3098 time to fit residues: 46.2501 Evaluate side-chains 84 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 46 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 205 VAL 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 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 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 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: 8.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.104447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.072505 restraints weight = 46000.374| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 6.99 r_work: 0.3489 rms_B_bonded: 6.26 restraints_weight: 2.0000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11852 Z= 0.208 Angle : 0.662 11.605 16173 Z= 0.327 Chirality : 0.046 0.264 1817 Planarity : 0.005 0.066 2085 Dihedral : 9.476 88.221 1825 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.51 % Rotamer: Outliers : 4.36 % Allowed : 17.15 % Favored : 78.49 % 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: -1.31 (0.22), residues: 1484 helix: -1.54 (0.68), residues: 47 sheet: -0.53 (0.25), residues: 418 loop : -1.01 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 393 HIS 0.004 0.001 HIS E 235 PHE 0.016 0.002 PHE E 454 TYR 0.017 0.002 TYR E 387 ARG 0.007 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 5) link_NAG-ASN : angle 3.04216 ( 15) link_BETA1-4 : bond 0.00710 ( 4) link_BETA1-4 : angle 2.29200 ( 12) hydrogen bonds : bond 0.03666 ( 299) hydrogen bonds : angle 5.91356 ( 783) SS BOND : bond 0.00310 ( 34) SS BOND : angle 0.95270 ( 68) covalent geometry : bond 0.00460 (11809) covalent geometry : angle 0.65181 (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 104 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 48 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: C 81 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7684 (mp0) REVERT: C 134 CYS cc_start: 0.6441 (t) cc_final: 0.6138 (t) REVERT: C 179 LEU cc_start: 0.8490 (tp) cc_final: 0.8218 (mt) REVERT: E 71 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7984 (pp30) REVERT: E 95 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 116 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7787 (ttm-80) REVERT: E 409 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8050 (tt) REVERT: E 466 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8706 (p0) outliers start: 56 outliers final: 40 residues processed: 99 average time/residue: 0.3037 time to fit residues: 44.3840 Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 44 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 204 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 PHE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 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: 1.9990 chunk 131 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 139 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** 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 = 0.4369 r_free = 0.4369 target = 0.105875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.074659 restraints weight = 46904.829| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 6.42 r_work: 0.3523 rms_B_bonded: 5.95 restraints_weight: 2.0000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2170 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= 0.124 Angle : 0.614 11.934 16173 Z= 0.300 Chirality : 0.044 0.258 1817 Planarity : 0.005 0.059 2085 Dihedral : 8.649 74.674 1825 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 3.98 % Allowed : 17.93 % 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: -1.23 (0.22), residues: 1484 helix: -1.99 (0.62), residues: 53 sheet: -0.47 (0.25), residues: 416 loop : -0.91 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 430 HIS 0.004 0.001 HIS E 327 PHE 0.015 0.001 PHE A 139 TYR 0.015 0.001 TYR A 92 ARG 0.002 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 3.08758 ( 15) link_BETA1-4 : bond 0.00564 ( 4) link_BETA1-4 : angle 2.39668 ( 12) hydrogen bonds : bond 0.03213 ( 299) hydrogen bonds : angle 5.74401 ( 783) SS BOND : bond 0.00238 ( 34) SS BOND : angle 0.78899 ( 68) covalent geometry : bond 0.00281 (11809) covalent geometry : angle 0.60240 (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 101 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 50 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7619 (mmm) cc_final: 0.6236 (mmm) REVERT: B 98 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (ptm160) REVERT: C 81 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7735 (mp0) REVERT: C 125 LEU cc_start: 0.7327 (mt) cc_final: 0.6919 (mt) REVERT: C 179 LEU cc_start: 0.8499 (tp) cc_final: 0.8208 (mt) REVERT: C 194 CYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5369 (p) REVERT: E 95 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8294 (pp) REVERT: E 409 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7941 (tt) REVERT: E 455 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6991 (p) REVERT: E 466 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8724 (p0) outliers start: 51 outliers final: 38 residues processed: 95 average time/residue: 0.2401 time to fit residues: 34.5781 Evaluate side-chains 90 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 46 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 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 205 VAL Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 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 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 159 LEU 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 455 VAL Chi-restraints excluded: chain E residue 466 ASN Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 94 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.4385 r_free = 0.4385 target = 0.106788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.075687 restraints weight = 46465.442| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 6.61 r_work: 0.3554 rms_B_bonded: 6.00 restraints_weight: 2.0000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11852 Z= 0.101 Angle : 0.586 10.580 16173 Z= 0.286 Chirality : 0.044 0.262 1817 Planarity : 0.005 0.049 2085 Dihedral : 7.091 56.972 1821 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 3.59 % Allowed : 19.02 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.23), residues: 1484 helix: -2.04 (0.62), residues: 55 sheet: -0.38 (0.25), residues: 444 loop : -0.81 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 430 HIS 0.005 0.001 HIS E 490 PHE 0.012 0.001 PHE A 139 TYR 0.016 0.001 TYR A 36 ARG 0.003 0.000 ARG E 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 5) link_NAG-ASN : angle 3.66721 ( 15) link_BETA1-4 : bond 0.00697 ( 4) link_BETA1-4 : angle 2.51230 ( 12) hydrogen bonds : bond 0.02948 ( 299) hydrogen bonds : angle 5.52102 ( 783) SS BOND : bond 0.00249 ( 34) SS BOND : angle 0.82767 ( 68) covalent geometry : bond 0.00232 (11809) covalent geometry : angle 0.57032 (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 95 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 49 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7539 (mmm) cc_final: 0.6325 (mmm) REVERT: B 98 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8185 (ptm160) REVERT: C 81 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7720 (mp0) REVERT: C 125 LEU cc_start: 0.7195 (mt) cc_final: 0.6807 (mt) REVERT: C 179 LEU cc_start: 0.8392 (tp) cc_final: 0.8086 (mt) REVERT: D 66 ARG cc_start: 0.5719 (OUTLIER) cc_final: 0.4632 (ptm160) REVERT: E 95 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (pp) outliers start: 46 outliers final: 35 residues processed: 87 average time/residue: 0.3408 time to fit residues: 45.9473 Evaluate side-chains 84 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 46 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 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 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 205 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 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 95 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 160 THR 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 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: 4.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 0.0060 chunk 116 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.0276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.106252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.074952 restraints weight = 46093.813| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 6.77 r_work: 0.3551 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2493 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= 0.116 Angle : 0.589 9.711 16173 Z= 0.289 Chirality : 0.044 0.261 1817 Planarity : 0.004 0.049 2085 Dihedral : 6.726 57.725 1815 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 3.74 % Allowed : 18.78 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.04 (0.23), residues: 1484 helix: -1.86 (0.66), residues: 55 sheet: -0.34 (0.25), residues: 437 loop : -0.78 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 430 HIS 0.004 0.001 HIS E 327 PHE 0.011 0.001 PHE A 139 TYR 0.017 0.001 TYR B 201 ARG 0.004 0.000 ARG E 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 5) link_NAG-ASN : angle 3.52669 ( 15) link_BETA1-4 : bond 0.00614 ( 4) link_BETA1-4 : angle 2.54638 ( 12) hydrogen bonds : bond 0.03026 ( 299) hydrogen bonds : angle 5.51594 ( 783) SS BOND : bond 0.00236 ( 34) SS BOND : angle 1.28046 ( 68) covalent geometry : bond 0.00264 (11809) covalent geometry : angle 0.57024 (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 96 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 48 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7541 (mmm) cc_final: 0.6074 (mmm) REVERT: B 87 ARG cc_start: 0.7244 (mpt-90) cc_final: 0.6837 (ptp90) REVERT: B 98 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8254 (ptm160) REVERT: C 179 LEU cc_start: 0.8442 (tp) cc_final: 0.8131 (mt) REVERT: D 66 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.3790 (ptm160) REVERT: E 71 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8031 (pp30) REVERT: E 95 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8239 (pp) outliers start: 48 outliers final: 38 residues processed: 89 average time/residue: 0.2931 time to fit residues: 39.7804 Evaluate side-chains 87 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 45 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 154 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 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 107 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** E 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.103122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.070937 restraints weight = 46758.091| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 6.78 r_work: 0.3436 rms_B_bonded: 6.28 restraints_weight: 2.0000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11852 Z= 0.288 Angle : 0.750 13.082 16173 Z= 0.374 Chirality : 0.047 0.257 1817 Planarity : 0.005 0.052 2085 Dihedral : 7.217 59.313 1814 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.37 % Favored : 90.57 % Rotamer: Outliers : 3.90 % Allowed : 19.25 % Favored : 76.85 % 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: -2.02 (0.61), residues: 58 sheet: -0.45 (0.26), residues: 413 loop : -1.15 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 460 HIS 0.007 0.001 HIS B 35 PHE 0.021 0.002 PHE E 454 TYR 0.025 0.002 TYR E 387 ARG 0.008 0.001 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 5) link_NAG-ASN : angle 3.54608 ( 15) link_BETA1-4 : bond 0.00663 ( 4) link_BETA1-4 : angle 2.62345 ( 12) hydrogen bonds : bond 0.04082 ( 299) hydrogen bonds : angle 6.06736 ( 783) SS BOND : bond 0.00375 ( 34) SS BOND : angle 1.54599 ( 68) covalent geometry : bond 0.00633 (11809) covalent geometry : angle 0.73426 (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 91 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 41 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7731 (mmm) cc_final: 0.6198 (mmm) REVERT: B 87 ARG cc_start: 0.7345 (mpt-90) cc_final: 0.6949 (ptp90) REVERT: C 179 LEU cc_start: 0.8377 (tp) cc_final: 0.8057 (mt) REVERT: E 71 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8335 (pp30) REVERT: E 95 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8186 (pp) REVERT: E 409 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7986 (tt) outliers start: 50 outliers final: 40 residues processed: 83 average time/residue: 0.2119 time to fit residues: 27.4886 Evaluate side-chains 82 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 39 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 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 148 TRP 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 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 23 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE 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: 0.3980 chunk 77 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** 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 = 0.4361 r_free = 0.4361 target = 0.105578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.074130 restraints weight = 45951.554| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 6.85 r_work: 0.3529 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2590 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= 0.122 Angle : 0.622 11.717 16173 Z= 0.308 Chirality : 0.044 0.247 1817 Planarity : 0.005 0.057 2085 Dihedral : 6.837 59.653 1814 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 3.20 % Allowed : 20.03 % 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: -1.17 (0.23), residues: 1484 helix: -1.80 (0.67), residues: 53 sheet: -0.47 (0.25), residues: 422 loop : -0.86 (0.21), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 430 HIS 0.003 0.001 HIS E 327 PHE 0.013 0.001 PHE A 139 TYR 0.018 0.001 TYR A 92 ARG 0.015 0.001 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 5) link_NAG-ASN : angle 3.11420 ( 15) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 2.59918 ( 12) hydrogen bonds : bond 0.03236 ( 299) hydrogen bonds : angle 5.76226 ( 783) SS BOND : bond 0.00243 ( 34) SS BOND : angle 1.15933 ( 68) covalent geometry : bond 0.00275 (11809) covalent geometry : angle 0.60783 (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 85 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 44 time to evaluate : 1.224 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: 0.6813 (mmm) REVERT: B 87 ARG cc_start: 0.7288 (mpt-90) cc_final: 0.6893 (ptp90) REVERT: C 179 LEU cc_start: 0.8455 (tp) cc_final: 0.8115 (mt) REVERT: E 71 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8248 (pp30) REVERT: E 95 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8230 (pp) REVERT: E 409 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7961 (tt) outliers start: 41 outliers final: 35 residues processed: 80 average time/residue: 0.1871 time to fit residues: 24.1579 Evaluate side-chains 79 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 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 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 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 480 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain E residue 519 VAL Chi-restraints excluded: chain E residue 549 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 30.0000 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.105537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.074268 restraints weight = 45937.800| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 6.50 r_work: 0.3527 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2640 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= 0.127 Angle : 0.616 11.504 16173 Z= 0.305 Chirality : 0.044 0.253 1817 Planarity : 0.005 0.062 2085 Dihedral : 6.731 59.523 1814 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 3.43 % Allowed : 19.88 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.23), residues: 1484 helix: -1.75 (0.68), residues: 53 sheet: -0.51 (0.25), residues: 437 loop : -0.82 (0.21), residues: 994 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 0.013 0.001 PHE A 139 TYR 0.015 0.001 TYR A 92 ARG 0.005 0.000 ARG D 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 5) link_NAG-ASN : angle 3.16120 ( 15) link_BETA1-4 : bond 0.00573 ( 4) link_BETA1-4 : angle 2.54703 ( 12) hydrogen bonds : bond 0.03170 ( 299) hydrogen bonds : angle 5.68099 ( 783) SS BOND : bond 0.00234 ( 34) SS BOND : angle 1.10612 ( 68) covalent geometry : bond 0.00287 (11809) covalent geometry : angle 0.60190 (16078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9896.07 seconds wall clock time: 179 minutes 5.41 seconds (10745.41 seconds total)