Starting phenix.real_space_refine on Wed Jun 18 22:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqy_47118/06_2025/9dqy_47118.cif" } resolution = 2.8 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= 0.002 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 126 5.16 5 C 13740 2.51 5 N 3691 2.21 5 O 4110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21667 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3279 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "B" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3150 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 26, 'TRANS': 374} Chain: "C" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3262 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 404} Chain breaks: 1 Chain: "D" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3150 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 26, 'TRANS': 374} Chain: "E" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3279 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "F" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3150 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 26, 'TRANS': 374} Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 14.48, per 1000 atoms: 0.67 Number of scatterers: 21667 At special positions: 0 Unit cell: (161.68, 158.86, 156.04, 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 126 16.00 O 4110 8.00 N 3691 7.00 C 13740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 25 " distance=2.02 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 266 " distance=2.04 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.04 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 25 " distance=2.02 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 266 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 226 " distance=2.03 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 73 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 73 " distance=2.03 Simple disulfide: pdb=" SG CYS I 67 " - pdb=" SG CYS I 73 " 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 NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG A 502 " - " ASN A 245 " " NAG B 501 " - " ASN B 196 " " NAG B 502 " - " ASN B 318 " " NAG C 501 " - " ASN C 139 " " NAG C 502 " - " ASN C 245 " " NAG D 501 " - " ASN D 196 " " NAG D 502 " - " ASN D 318 " " NAG E 501 " - " ASN E 139 " " NAG E 502 " - " ASN E 245 " " NAG F 501 " - " ASN F 196 " " NAG F 502 " - " ASN F 318 " Time building additional restraints: 4.76 Conformation dependent library (CDL) restraints added in 2.8 seconds 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5180 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 64 sheets defined 13.5% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.274A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.711A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.051A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 434 removed outlier: 3.601A pdb=" N LEU A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.524A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 398 Processing helix chain 'C' and resid 111 through 116 removed outlier: 4.292A pdb=" N THR C 115 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 116 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.955A pdb=" N GLY C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 403 through 433 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 351 through 363 removed outlier: 3.529A pdb=" N ILE D 355 " --> pdb=" O TRP D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 398 removed outlier: 3.511A pdb=" N THR D 367 " --> pdb=" O HIS D 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.303A pdb=" N THR E 115 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.913A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS E 259 " --> pdb=" O PRO E 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 259' Processing helix chain 'E' and resid 406 through 434 removed outlier: 3.542A pdb=" N LEU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.795A pdb=" N LEU F 8 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 398 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 26 through 33 removed outlier: 4.098A pdb=" N SER G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 Processing helix chain 'H' and resid 19 through 23 Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 26 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.517A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.852A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.509A pdb=" N MET A 88 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 304 removed outlier: 5.023A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.375A pdb=" N LEU B 285 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE B 319 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 287 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG B 317 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA B 289 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR B 315 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG B 291 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY B 313 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.426A pdb=" N HIS B 256 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY B 253 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR B 167 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 255 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 165 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 257 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB5, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.552A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N SER B 48 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET B 67 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS B 63 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.552A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR B 99 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ALA B 49 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS B 97 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N PHE B 51 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N GLY B 95 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 15.385A pdb=" N TYR B 53 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 17.977A pdb=" N ARG B 93 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.408A pdb=" N ASP B 109 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AB9, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AC2, first strand: chain 'C' and resid 2 through 8 removed outlier: 4.672A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 161 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 15 through 19 removed outlier: 5.477A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 35 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 128 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 140 through 148 removed outlier: 4.701A pdb=" N LEU C 129 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 128 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 35 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.788A pdb=" N ASN C 100 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AC8, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'C' and resid 296 through 304 removed outlier: 4.584A pdb=" N GLU C 298 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 321 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 315 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AD2, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AD3, first strand: chain 'D' and resid 2 through 3 removed outlier: 5.872A pdb=" N LYS D 254 " --> pdb=" O THR D 3 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AD5, first strand: chain 'D' and resid 31 through 35 removed outlier: 3.892A pdb=" N ASN D 33 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN D 104 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG D 93 " --> pdb=" O GLN D 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 50 through 53 removed outlier: 11.916A pdb=" N GLN D 50 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N THR D 62 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY D 52 " --> pdb=" O ASP D 60 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.263A pdb=" N ASP D 109 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 150 through 155 Processing sheet with id=AD9, first strand: chain 'D' and resid 180 through 183 removed outlier: 3.855A pdb=" N THR D 215 " --> pdb=" O ILE D 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 206 through 211 Processing sheet with id=AE2, first strand: chain 'D' and resid 275 through 276 removed outlier: 3.621A pdb=" N THR D 275 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AE4, first strand: chain 'E' and resid 12 through 19 removed outlier: 4.430A pdb=" N VAL E 33 " --> pdb=" O GLY E 12 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE E 31 " --> pdb=" O PRO E 14 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS E 16 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU E 29 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU E 18 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU E 27 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE E 31 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 35 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR E 126 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN E 43 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU E 45 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL E 47 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 140 through 148 removed outlier: 4.622A pdb=" N LEU E 129 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL E 47 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU E 45 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN E 43 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR E 126 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 35 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE E 31 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AE7, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.015A pdb=" N ASN E 100 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF1, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AF2, first strand: chain 'E' and resid 299 through 304 removed outlier: 3.777A pdb=" N SER E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 306 through 307 removed outlier: 7.156A pdb=" N CYS E 306 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 366 " --> pdb=" O HIS E 333 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 306 through 307 removed outlier: 7.156A pdb=" N CYS E 306 " --> pdb=" O LYS E 381 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AF6, first strand: chain 'E' and resid 387 through 388 removed outlier: 7.416A pdb=" N LEU F 285 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE F 319 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU F 287 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG F 317 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA F 289 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 315 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG F 291 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY F 313 " --> pdb=" O ARG F 291 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.486A pdb=" N HIS F 256 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY F 253 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR F 167 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU F 255 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR F 165 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE F 257 " --> pdb=" O ALA F 163 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AF9, first strand: chain 'F' and resid 31 through 35 removed outlier: 3.865A pdb=" N ASN F 33 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE F 100 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N HIS F 96 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU F 102 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE F 85 " --> pdb=" O CYS F 91 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG F 93 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N ILE F 83 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP F 109 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 50 through 53 removed outlier: 5.838A pdb=" N LYS F 63 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 150 through 155 Processing sheet with id=AG3, first strand: chain 'F' and resid 180 through 182 removed outlier: 4.303A pdb=" N VAL F 187 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 206 through 211 Processing sheet with id=AG5, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AG6, first strand: chain 'G' and resid 15 through 18 removed outlier: 7.456A pdb=" N PHE G 15 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL G 57 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 54 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.059A pdb=" N LEU H 2 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU H 93 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR H 4 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN H 36 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 15 through 18 removed outlier: 7.283A pdb=" N PHE H 15 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL H 57 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY H 17 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 4 through 7 removed outlier: 6.219A pdb=" N TYR I 4 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU I 95 " --> pdb=" O TYR I 4 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL I 6 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN I 36 " --> pdb=" O PHE I 80 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 15 through 18 removed outlier: 7.520A pdb=" N PHE I 15 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL I 57 " --> pdb=" O PHE I 15 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2133 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: 8.03 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6924 1.34 - 1.46: 5364 1.46 - 1.59: 9780 1.59 - 1.72: 0 1.72 - 1.84: 150 Bond restraints: 22218 Sorted by residual: bond pdb=" C LEU F 141 " pdb=" N LEU F 142 " ideal model delta sigma weight residual 1.329 1.283 0.045 1.35e-02 5.49e+03 1.13e+01 bond pdb=" N LEU I 87 " pdb=" CA LEU I 87 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.39e+00 bond pdb=" N GLU H 78 " pdb=" CA GLU H 78 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.25e-02 6.40e+03 4.88e+00 bond pdb=" CB ASN C 139 " pdb=" CG ASN C 139 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CB GLU C 264 " pdb=" CG GLU C 264 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.66e+00 ... (remaining 22213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 30063 3.62 - 7.25: 168 7.25 - 10.87: 21 10.87 - 14.49: 4 14.49 - 18.12: 1 Bond angle restraints: 30257 Sorted by residual: angle pdb=" CA GLU C 264 " pdb=" CB GLU C 264 " pdb=" CG GLU C 264 " ideal model delta sigma weight residual 114.10 124.70 -10.60 2.00e+00 2.50e-01 2.81e+01 angle pdb=" CA LEU B 8 " pdb=" CB LEU B 8 " pdb=" CG LEU B 8 " ideal model delta sigma weight residual 116.30 134.42 -18.12 3.50e+00 8.16e-02 2.68e+01 angle pdb=" C2 NAG B 501 " pdb=" N2 NAG B 501 " pdb=" C7 NAG B 501 " ideal model delta sigma weight residual 124.56 136.67 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C2 NAG D 501 " pdb=" N2 NAG D 501 " pdb=" C7 NAG D 501 " ideal model delta sigma weight residual 124.56 136.58 -12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C2 NAG F 501 " pdb=" N2 NAG F 501 " pdb=" C7 NAG F 501 " ideal model delta sigma weight residual 124.56 136.48 -11.92 3.00e+00 1.11e-01 1.58e+01 ... (remaining 30252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12435 17.83 - 35.66: 860 35.66 - 53.49: 134 53.49 - 71.32: 54 71.32 - 89.15: 16 Dihedral angle restraints: 13499 sinusoidal: 5445 harmonic: 8054 Sorted by residual: dihedral pdb=" CB CYS B 152 " pdb=" SG CYS B 152 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual 93.00 168.56 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS D 152 " pdb=" SG CYS D 152 " pdb=" SG CYS D 266 " pdb=" CB CYS D 266 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS F 152 " pdb=" SG CYS F 152 " pdb=" SG CYS F 266 " pdb=" CB CYS F 266 " ideal model delta sinusoidal sigma weight residual 93.00 168.07 -75.07 1 1.00e+01 1.00e-02 7.13e+01 ... (remaining 13496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3092 0.088 - 0.175: 350 0.175 - 0.263: 14 0.263 - 0.350: 5 0.350 - 0.438: 2 Chirality restraints: 3463 Sorted by residual: chirality pdb=" CB ILE E 307 " pdb=" CA ILE E 307 " pdb=" CG1 ILE E 307 " pdb=" CG2 ILE E 307 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CG LEU B 287 " pdb=" CB LEU B 287 " pdb=" CD1 LEU B 287 " pdb=" CD2 LEU B 287 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C2 NAG F 501 " pdb=" C1 NAG F 501 " pdb=" C3 NAG F 501 " pdb=" N2 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3460 not shown) Planarity restraints: 3872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 137 " -0.256 9.50e-02 1.11e+02 1.15e-01 8.22e+00 pdb=" NE ARG D 137 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 137 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 137 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 160 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C LYS E 160 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS E 160 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL E 161 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.168 9.50e-02 1.11e+02 7.55e-02 3.53e+00 pdb=" NE ARG B 137 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.005 2.00e-02 2.50e+03 ... (remaining 3869 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2282 2.75 - 3.29: 20210 3.29 - 3.83: 36136 3.83 - 4.36: 41961 4.36 - 4.90: 74572 Nonbonded interactions: 175161 Sorted by model distance: nonbonded pdb=" O ARG B 394 " pdb=" OG1 THR B 398 " model vdw 2.216 3.040 nonbonded pdb=" CG2 THR F 23 " pdb=" NE ARG H 89 " model vdw 2.237 3.540 nonbonded pdb=" OG SER F 79 " pdb=" OE1 GLU F 81 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OD1 ASP A 311 " model vdw 2.256 3.040 nonbonded pdb=" OG SER D 27 " pdb=" O ILE D 29 " model vdw 2.262 3.040 ... (remaining 175156 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 155 or resid 158 through 434 or resid 501 throug \ h 502)) selection = chain 'C' selection = (chain 'E' and (resid 1 through 155 or resid 158 through 434 or resid 501 throug \ h 502)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.480 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22275 Z= 0.168 Angle : 0.788 18.117 30383 Z= 0.403 Chirality : 0.054 0.438 3463 Planarity : 0.005 0.115 3860 Dihedral : 12.440 89.148 8184 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2750 helix: 0.46 (0.27), residues: 316 sheet: 0.06 (0.17), residues: 964 loop : -0.76 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 279 HIS 0.011 0.001 HIS I 3 PHE 0.028 0.002 PHE D 134 TYR 0.022 0.001 TYR E 308 ARG 0.006 0.001 ARG D 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 12) link_NAG-ASN : angle 2.24674 ( 36) hydrogen bonds : bond 0.11740 ( 766) hydrogen bonds : angle 6.09898 ( 2133) SS BOND : bond 0.00461 ( 45) SS BOND : angle 1.71659 ( 90) covalent geometry : bond 0.00355 (22218) covalent geometry : angle 0.78027 (30257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9093 (pm20) cc_final: 0.8687 (pm20) REVERT: A 351 SER cc_start: 0.9186 (p) cc_final: 0.8676 (t) REVERT: C 24 TYR cc_start: 0.9056 (m-80) cc_final: 0.8174 (m-80) REVERT: C 160 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8504 (mmmt) REVERT: D 129 LYS cc_start: 0.9271 (tttm) cc_final: 0.8905 (tptm) REVERT: F 71 HIS cc_start: 0.8516 (p-80) cc_final: 0.8281 (p-80) REVERT: F 129 LYS cc_start: 0.9099 (tttm) cc_final: 0.8887 (tptm) REVERT: G 86 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7728 (mt-10) REVERT: G 91 GLU cc_start: 0.5129 (mt-10) cc_final: 0.4422 (mt-10) REVERT: H 74 LEU cc_start: 0.7642 (mt) cc_final: 0.7345 (mt) REVERT: H 78 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6992 (mt-10) REVERT: H 86 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7934 (mt-10) outliers start: 0 outliers final: 2 residues processed: 308 average time/residue: 1.3317 time to fit residues: 466.7113 Evaluate side-chains 217 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.0570 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 250 optimal weight: 30.0000 overall best weight: 4.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 230 HIS B 71 HIS B 218 ASN C 230 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 230 HIS F 252 GLN F 349 HIS G 10 GLN G 12 HIS G 58 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.064137 restraints weight = 46491.527| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.03 r_work: 0.2517 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 22275 Z= 0.257 Angle : 0.652 12.309 30383 Z= 0.330 Chirality : 0.048 0.296 3463 Planarity : 0.004 0.058 3860 Dihedral : 6.462 92.981 3246 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 1.43 % Allowed : 6.84 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2750 helix: 1.35 (0.28), residues: 315 sheet: -0.09 (0.16), residues: 1019 loop : -0.58 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.006 0.001 HIS B 71 PHE 0.023 0.002 PHE D 134 TYR 0.020 0.001 TYR E 308 ARG 0.008 0.001 ARG F 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 12) link_NAG-ASN : angle 2.40683 ( 36) hydrogen bonds : bond 0.03685 ( 766) hydrogen bonds : angle 4.98535 ( 2133) SS BOND : bond 0.00471 ( 45) SS BOND : angle 1.67550 ( 90) covalent geometry : bond 0.00600 (22218) covalent geometry : angle 0.64139 (30257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9062 (pm20) cc_final: 0.8618 (pm20) REVERT: A 407 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.7590 (t60) REVERT: C 24 TYR cc_start: 0.8946 (m-80) cc_final: 0.8529 (m-80) REVERT: C 160 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8463 (mmmt) REVERT: C 264 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8788 (pp20) REVERT: D 129 LYS cc_start: 0.9375 (tttm) cc_final: 0.8950 (tptm) REVERT: E 96 CYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7584 (m) REVERT: F 71 HIS cc_start: 0.8589 (p-80) cc_final: 0.8361 (p-80) REVERT: F 129 LYS cc_start: 0.9305 (tttm) cc_final: 0.9070 (tptp) REVERT: G 78 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7160 (mt-10) REVERT: G 86 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7723 (mt-10) REVERT: H 86 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7634 (mt-10) REVERT: I 9 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7267 (mm-30) outliers start: 34 outliers final: 10 residues processed: 241 average time/residue: 1.1763 time to fit residues: 327.6787 Evaluate side-chains 219 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 50 optimal weight: 3.9990 chunk 250 optimal weight: 40.0000 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 149 GLN E 230 HIS E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.065126 restraints weight = 46486.052| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.01 r_work: 0.2538 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22275 Z= 0.168 Angle : 0.589 10.804 30383 Z= 0.296 Chirality : 0.046 0.271 3463 Planarity : 0.004 0.038 3860 Dihedral : 5.884 58.115 3242 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 1.22 % Allowed : 8.06 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2750 helix: 1.71 (0.28), residues: 313 sheet: -0.01 (0.16), residues: 1005 loop : -0.58 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 330 HIS 0.010 0.001 HIS E 230 PHE 0.015 0.001 PHE D 134 TYR 0.016 0.001 TYR E 308 ARG 0.005 0.000 ARG D 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 12) link_NAG-ASN : angle 2.03625 ( 36) hydrogen bonds : bond 0.03404 ( 766) hydrogen bonds : angle 4.79565 ( 2133) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.28653 ( 90) covalent geometry : bond 0.00388 (22218) covalent geometry : angle 0.58176 (30257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9021 (pm20) cc_final: 0.8622 (pm20) REVERT: A 407 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7527 (t60) REVERT: C 24 TYR cc_start: 0.8941 (m-80) cc_final: 0.8493 (m-80) REVERT: C 160 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8394 (mmmt) REVERT: C 264 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8734 (pp20) REVERT: D 129 LYS cc_start: 0.9341 (tttm) cc_final: 0.8903 (tptm) REVERT: F 71 HIS cc_start: 0.8590 (p-80) cc_final: 0.8390 (p-80) REVERT: F 129 LYS cc_start: 0.9244 (tttm) cc_final: 0.8982 (tptp) REVERT: G 78 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7150 (mt-10) REVERT: G 85 LEU cc_start: 0.7850 (mt) cc_final: 0.7622 (tp) REVERT: G 86 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7763 (mt-10) REVERT: H 78 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7128 (mt-10) REVERT: H 86 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7794 (mt-10) REVERT: I 9 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7240 (mm-30) outliers start: 29 outliers final: 13 residues processed: 232 average time/residue: 1.2256 time to fit residues: 328.6354 Evaluate side-chains 218 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 119 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 109 optimal weight: 0.0000 chunk 212 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 164 optimal weight: 30.0000 overall best weight: 3.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.063327 restraints weight = 46891.864| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.03 r_work: 0.2499 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22275 Z= 0.230 Angle : 0.608 10.407 30383 Z= 0.307 Chirality : 0.047 0.275 3463 Planarity : 0.004 0.037 3860 Dihedral : 5.806 58.029 3242 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 1.55 % Allowed : 9.36 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2750 helix: 1.84 (0.28), residues: 315 sheet: -0.02 (0.16), residues: 1006 loop : -0.54 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 330 HIS 0.005 0.001 HIS B 71 PHE 0.018 0.001 PHE D 134 TYR 0.020 0.001 TYR E 308 ARG 0.007 0.000 ARG D 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 2.15284 ( 36) hydrogen bonds : bond 0.03450 ( 766) hydrogen bonds : angle 4.76203 ( 2133) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.43866 ( 90) covalent geometry : bond 0.00537 (22218) covalent geometry : angle 0.59980 (30257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8937 (pm20) cc_final: 0.8551 (pm20) REVERT: A 407 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7581 (t60) REVERT: C 160 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8439 (mmmt) REVERT: C 264 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8819 (pp20) REVERT: C 327 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.5572 (p-80) REVERT: D 129 LYS cc_start: 0.9358 (tttm) cc_final: 0.8902 (tptm) REVERT: D 337 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8733 (mtt90) REVERT: F 20 ARG cc_start: 0.8748 (ppt170) cc_final: 0.8435 (ptm-80) REVERT: F 71 HIS cc_start: 0.8574 (p-80) cc_final: 0.8344 (p-80) REVERT: F 134 PHE cc_start: 0.6750 (m-80) cc_final: 0.6507 (m-10) REVERT: G 2 LEU cc_start: 0.6468 (mm) cc_final: 0.6083 (mt) REVERT: G 78 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7187 (mt-10) REVERT: H 78 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7125 (mt-10) REVERT: H 86 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7792 (mt-10) REVERT: I 9 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7187 (mm-30) outliers start: 37 outliers final: 23 residues processed: 227 average time/residue: 1.2321 time to fit residues: 322.9245 Evaluate side-chains 223 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 209 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 273 optimal weight: 0.0030 chunk 230 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 225 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN D 363 HIS E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.065819 restraints weight = 46356.709| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.94 r_work: 0.2550 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22275 Z= 0.113 Angle : 0.561 9.804 30383 Z= 0.281 Chirality : 0.045 0.260 3463 Planarity : 0.003 0.037 3860 Dihedral : 5.473 58.245 3242 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.34 % Allowed : 10.70 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2750 helix: 1.94 (0.28), residues: 315 sheet: -0.05 (0.16), residues: 1023 loop : -0.50 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 89 HIS 0.005 0.000 HIS B 71 PHE 0.010 0.001 PHE B 64 TYR 0.012 0.001 TYR E 308 ARG 0.006 0.000 ARG D 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.80947 ( 36) hydrogen bonds : bond 0.03112 ( 766) hydrogen bonds : angle 4.59372 ( 2133) SS BOND : bond 0.00193 ( 45) SS BOND : angle 1.03794 ( 90) covalent geometry : bond 0.00251 (22218) covalent geometry : angle 0.55623 (30257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8874 (pm20) cc_final: 0.8508 (pm20) REVERT: A 407 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7588 (t60) REVERT: C 160 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8449 (mmmt) REVERT: C 264 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8830 (pp20) REVERT: D 129 LYS cc_start: 0.9335 (tttm) cc_final: 0.8875 (tptm) REVERT: D 239 ASN cc_start: 0.8798 (p0) cc_final: 0.8579 (p0) REVERT: F 71 HIS cc_start: 0.8565 (p-80) cc_final: 0.8338 (p-80) REVERT: G 2 LEU cc_start: 0.6323 (mm) cc_final: 0.5910 (mt) REVERT: G 78 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7134 (mt-10) REVERT: H 78 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6948 (mt-10) REVERT: H 86 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7795 (mt-10) REVERT: I 9 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7192 (mm-30) outliers start: 32 outliers final: 16 residues processed: 233 average time/residue: 1.2383 time to fit residues: 333.0978 Evaluate side-chains 223 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 263 optimal weight: 20.0000 chunk 104 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 74 optimal weight: 0.0670 chunk 41 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.064288 restraints weight = 46145.342| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.02 r_work: 0.2522 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22275 Z= 0.175 Angle : 0.584 9.779 30383 Z= 0.292 Chirality : 0.046 0.267 3463 Planarity : 0.003 0.041 3860 Dihedral : 5.482 58.186 3242 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 1.55 % Allowed : 10.95 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2750 helix: 2.01 (0.29), residues: 315 sheet: -0.01 (0.16), residues: 1019 loop : -0.49 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 351 HIS 0.005 0.001 HIS B 71 PHE 0.035 0.001 PHE F 134 TYR 0.017 0.001 TYR E 308 ARG 0.007 0.000 ARG F 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 12) link_NAG-ASN : angle 1.93321 ( 36) hydrogen bonds : bond 0.03208 ( 766) hydrogen bonds : angle 4.57983 ( 2133) SS BOND : bond 0.00311 ( 45) SS BOND : angle 1.18815 ( 90) covalent geometry : bond 0.00405 (22218) covalent geometry : angle 0.57769 (30257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8896 (pm20) cc_final: 0.8544 (pm20) REVERT: A 407 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7580 (t60) REVERT: C 160 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8416 (mmmt) REVERT: C 264 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8821 (pp20) REVERT: D 129 LYS cc_start: 0.9350 (tttm) cc_final: 0.8879 (tptm) REVERT: F 20 ARG cc_start: 0.8688 (ppt170) cc_final: 0.8411 (ptm-80) REVERT: F 71 HIS cc_start: 0.8571 (p-80) cc_final: 0.8329 (p-80) REVERT: G 78 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7080 (mt-10) REVERT: H 78 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6941 (mt-10) REVERT: H 86 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7734 (mt-10) REVERT: I 9 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7147 (mm-30) outliers start: 37 outliers final: 19 residues processed: 229 average time/residue: 1.2187 time to fit residues: 322.6510 Evaluate side-chains 213 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 128 optimal weight: 10.0000 chunk 252 optimal weight: 30.0000 chunk 188 optimal weight: 0.0040 chunk 37 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 181 optimal weight: 0.0370 chunk 267 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.063908 restraints weight = 46687.482| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.90 r_work: 0.2489 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22275 Z= 0.242 Angle : 0.624 9.859 30383 Z= 0.313 Chirality : 0.047 0.274 3463 Planarity : 0.004 0.045 3860 Dihedral : 5.643 57.576 3242 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 1.72 % Allowed : 11.58 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2750 helix: 2.01 (0.29), residues: 315 sheet: -0.02 (0.16), residues: 1015 loop : -0.49 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.006 0.001 HIS B 71 PHE 0.030 0.001 PHE F 134 TYR 0.020 0.001 TYR E 308 ARG 0.009 0.001 ARG F 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 12) link_NAG-ASN : angle 2.09391 ( 36) hydrogen bonds : bond 0.03390 ( 766) hydrogen bonds : angle 4.65806 ( 2133) SS BOND : bond 0.00410 ( 45) SS BOND : angle 1.43637 ( 90) covalent geometry : bond 0.00564 (22218) covalent geometry : angle 0.61624 (30257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8449 (p-80) REVERT: A 407 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7607 (t60) REVERT: C 160 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8487 (mmmt) REVERT: C 264 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8811 (pp20) REVERT: D 129 LYS cc_start: 0.9348 (tttm) cc_final: 0.8859 (tptm) REVERT: F 20 ARG cc_start: 0.8771 (ppt170) cc_final: 0.8424 (ptm-80) REVERT: F 71 HIS cc_start: 0.8563 (p-80) cc_final: 0.8337 (p-80) REVERT: G 78 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7252 (mt-10) REVERT: H 78 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7146 (mt-10) REVERT: H 86 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7806 (mt-10) REVERT: I 9 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 41 outliers final: 27 residues processed: 220 average time/residue: 1.2947 time to fit residues: 330.3396 Evaluate side-chains 217 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.064940 restraints weight = 46581.804| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.99 r_work: 0.2529 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22275 Z= 0.131 Angle : 0.583 9.561 30383 Z= 0.291 Chirality : 0.046 0.263 3463 Planarity : 0.003 0.045 3860 Dihedral : 5.443 57.651 3242 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.34 % Allowed : 12.55 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2750 helix: 2.05 (0.29), residues: 315 sheet: -0.07 (0.16), residues: 1025 loop : -0.51 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.007 0.001 HIS D 71 PHE 0.020 0.001 PHE F 134 TYR 0.014 0.001 TYR E 308 ARG 0.010 0.000 ARG F 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 12) link_NAG-ASN : angle 1.83858 ( 36) hydrogen bonds : bond 0.03107 ( 766) hydrogen bonds : angle 4.53662 ( 2133) SS BOND : bond 0.00217 ( 45) SS BOND : angle 1.06845 ( 90) covalent geometry : bond 0.00300 (22218) covalent geometry : angle 0.57807 (30257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7579 (t60) REVERT: C 160 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8456 (mmmt) REVERT: C 264 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8677 (pp20) REVERT: D 129 LYS cc_start: 0.9339 (tttm) cc_final: 0.8875 (tptm) REVERT: D 239 ASN cc_start: 0.8838 (p0) cc_final: 0.8581 (p0) REVERT: F 20 ARG cc_start: 0.8713 (ppt170) cc_final: 0.8445 (ptm-80) REVERT: F 71 HIS cc_start: 0.8539 (p-80) cc_final: 0.8317 (p-80) REVERT: G 2 LEU cc_start: 0.6261 (mm) cc_final: 0.5768 (mt) REVERT: G 78 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7110 (mt-10) REVERT: H 78 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6965 (mt-10) REVERT: H 86 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7787 (mt-10) REVERT: I 9 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7153 (mm-30) outliers start: 32 outliers final: 21 residues processed: 220 average time/residue: 1.9735 time to fit residues: 501.0708 Evaluate side-chains 213 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 213 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS D 149 GLN E 364 ASN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.064960 restraints weight = 46322.333| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.85 r_work: 0.2526 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22275 Z= 0.171 Angle : 0.606 9.641 30383 Z= 0.303 Chirality : 0.046 0.265 3463 Planarity : 0.004 0.062 3860 Dihedral : 5.468 57.505 3242 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 1.43 % Allowed : 12.76 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2750 helix: 2.07 (0.29), residues: 315 sheet: -0.11 (0.16), residues: 1038 loop : -0.50 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.011 0.001 HIS D 71 PHE 0.022 0.001 PHE F 134 TYR 0.017 0.001 TYR E 308 ARG 0.013 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 12) link_NAG-ASN : angle 1.88845 ( 36) hydrogen bonds : bond 0.03172 ( 766) hydrogen bonds : angle 4.51350 ( 2133) SS BOND : bond 0.00286 ( 45) SS BOND : angle 1.16296 ( 90) covalent geometry : bond 0.00399 (22218) covalent geometry : angle 0.60062 (30257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7603 (t60) REVERT: C 160 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8498 (mmmt) REVERT: C 264 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8656 (pp20) REVERT: D 129 LYS cc_start: 0.9276 (tttm) cc_final: 0.8790 (tptm) REVERT: D 337 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8704 (mtt90) REVERT: F 71 HIS cc_start: 0.8534 (p-80) cc_final: 0.8310 (p-80) REVERT: G 78 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7303 (mt-10) REVERT: H 78 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7139 (mt-10) REVERT: H 86 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7899 (mt-10) REVERT: H 91 GLU cc_start: 0.4944 (mt-10) cc_final: 0.4727 (mt-10) REVERT: I 9 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7197 (mm-30) outliers start: 34 outliers final: 23 residues processed: 212 average time/residue: 1.8875 time to fit residues: 458.8369 Evaluate side-chains 213 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 41 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS E 364 ASN F 341 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.062172 restraints weight = 47106.501| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.00 r_work: 0.2464 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 22275 Z= 0.319 Angle : 0.676 10.155 30383 Z= 0.340 Chirality : 0.049 0.281 3463 Planarity : 0.004 0.058 3860 Dihedral : 5.743 57.701 3242 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.16 % Favored : 94.73 % Rotamer: Outliers : 1.43 % Allowed : 12.97 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2750 helix: 1.96 (0.29), residues: 311 sheet: -0.02 (0.16), residues: 1001 loop : -0.55 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 351 HIS 0.011 0.001 HIS D 71 PHE 0.035 0.002 PHE F 134 TYR 0.024 0.001 TYR E 308 ARG 0.015 0.001 ARG E 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 12) link_NAG-ASN : angle 2.19690 ( 36) hydrogen bonds : bond 0.03517 ( 766) hydrogen bonds : angle 4.67760 ( 2133) SS BOND : bond 0.00493 ( 45) SS BOND : angle 1.61265 ( 90) covalent geometry : bond 0.00748 (22218) covalent geometry : angle 0.66693 (30257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5500 Ramachandran restraints generated. 2750 Oldfield, 0 Emsley, 2750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (p-80) REVERT: A 362 GLN cc_start: 0.8548 (pt0) cc_final: 0.8334 (mt0) REVERT: A 407 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7606 (t60) REVERT: B 20 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8561 (ptp90) REVERT: C 160 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8456 (mmmt) REVERT: C 264 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8653 (pp20) REVERT: C 281 ASP cc_start: 0.8661 (p0) cc_final: 0.8451 (p0) REVERT: D 337 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8723 (mtt90) REVERT: F 20 ARG cc_start: 0.8772 (ppt170) cc_final: 0.8489 (ptm-80) REVERT: F 71 HIS cc_start: 0.8563 (p-80) cc_final: 0.8326 (p-80) REVERT: G 78 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7147 (mt-10) REVERT: H 78 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7043 (mt-10) REVERT: I 9 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7078 (mm-30) outliers start: 34 outliers final: 24 residues processed: 211 average time/residue: 1.3802 time to fit residues: 338.3236 Evaluate side-chains 218 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 240 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS E 364 ASN E 396 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.063835 restraints weight = 46741.452| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.99 r_work: 0.2499 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22275 Z= 0.173 Angle : 0.620 10.086 30383 Z= 0.311 Chirality : 0.046 0.271 3463 Planarity : 0.004 0.057 3860 Dihedral : 5.596 57.043 3242 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 1.13 % Allowed : 13.43 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2750 helix: 1.97 (0.29), residues: 311 sheet: -0.11 (0.16), residues: 1043 loop : -0.54 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.012 0.001 HIS D 71 PHE 0.042 0.001 PHE F 134 TYR 0.017 0.001 TYR E 308 ARG 0.011 0.000 ARG F 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 12) link_NAG-ASN : angle 1.96024 ( 36) hydrogen bonds : bond 0.03246 ( 766) hydrogen bonds : angle 4.58977 ( 2133) SS BOND : bond 0.00295 ( 45) SS BOND : angle 1.22224 ( 90) covalent geometry : bond 0.00402 (22218) covalent geometry : angle 0.61392 (30257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17864.66 seconds wall clock time: 313 minutes 42.20 seconds (18822.20 seconds total)