Starting phenix.real_space_refine on Fri Sep 19 00:55:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqy_47118/09_2025/9dqy_47118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqy_47118/09_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_47118/09_2025/9dqy_47118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqy_47118/09_2025/9dqy_47118.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqy_47118/09_2025/9dqy_47118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqy_47118/09_2025/9dqy_47118.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.31, per 1000 atoms: 0.25 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: 1.67 Conformation dependent library (CDL) restraints added in 950.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.09 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: 4.41 Time building geometry restraints manager: 2.27 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 502)) selection = chain 'C' selection = (chain 'E' and (resid 1 through 155 or resid 158 through 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.001 ARG D 137 TYR 0.022 0.001 TYR E 308 PHE 0.028 0.002 PHE D 134 TRP 0.030 0.001 TRP D 279 HIS 0.011 0.001 HIS I 3 Details of bonding type rmsd covalent geometry : bond 0.00355 (22218) covalent geometry : angle 0.78027 (30257) SS BOND : bond 0.00461 ( 45) SS BOND : angle 1.71659 ( 90) hydrogen bonds : bond 0.11740 ( 766) hydrogen bonds : angle 6.09898 ( 2133) link_NAG-ASN : bond 0.00385 ( 12) link_NAG-ASN : angle 2.24674 ( 36) *********************** 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 : 0.732 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: 0.6436 time to fit residues: 224.7327 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 : 0.815 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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 B 225 GLN C 230 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3262 r_free = 0.3262 target = 0.093391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.061692 restraints weight = 46756.654| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.03 r_work: 0.2461 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 22275 Z= 0.389 Angle : 0.733 12.950 30383 Z= 0.375 Chirality : 0.052 0.315 3463 Planarity : 0.005 0.063 3860 Dihedral : 6.684 83.841 3246 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 1.68 % Allowed : 6.88 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.16), residues: 2750 helix: 1.34 (0.28), residues: 315 sheet: -0.11 (0.16), residues: 1010 loop : -0.66 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 65 TYR 0.024 0.002 TYR E 273 PHE 0.031 0.002 PHE D 134 TRP 0.013 0.002 TRP D 279 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00907 (22218) covalent geometry : angle 0.71909 (30257) SS BOND : bond 0.00633 ( 45) SS BOND : angle 2.06630 ( 90) hydrogen bonds : bond 0.04024 ( 766) hydrogen bonds : angle 5.13556 ( 2133) link_NAG-ASN : bond 0.00398 ( 12) link_NAG-ASN : angle 2.80108 ( 36) *********************** 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 258 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.849 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: 0.9042 (pm20) cc_final: 0.8670 (pm20) REVERT: A 372 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8842 (ttpp) REVERT: A 402 VAL cc_start: 0.9087 (p) cc_final: 0.8803 (p) REVERT: A 407 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.7643 (t60) REVERT: C 160 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8478 (mmmt) REVERT: C 264 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8716 (pp20) REVERT: D 129 LYS cc_start: 0.9389 (tttm) cc_final: 0.8932 (tptm) REVERT: D 291 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (mtp180) REVERT: E 96 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7626 (m) REVERT: F 71 HIS cc_start: 0.8609 (p-80) cc_final: 0.8370 (p-80) REVERT: F 129 LYS cc_start: 0.9278 (tttm) cc_final: 0.8987 (tptp) REVERT: G 78 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7149 (mt-10) REVERT: G 86 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7698 (mt-10) REVERT: H 86 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7788 (mt-10) REVERT: I 9 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 40 outliers final: 19 residues processed: 240 average time/residue: 0.5807 time to fit residues: 160.1932 Evaluate side-chains 225 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 318 LEU Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 278 ILE 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 11 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 D 225 GLN E 43 ASN E 230 HIS E 364 ASN E 396 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.062803 restraints weight = 46860.570| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 3.00 r_work: 0.2473 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22275 Z= 0.253 Angle : 0.635 11.380 30383 Z= 0.322 Chirality : 0.048 0.283 3463 Planarity : 0.004 0.040 3860 Dihedral : 6.132 57.442 3242 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 1.72 % Allowed : 8.56 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2750 helix: 1.68 (0.28), residues: 313 sheet: -0.07 (0.16), residues: 1005 loop : -0.59 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 65 TYR 0.020 0.001 TYR E 308 PHE 0.031 0.001 PHE F 134 TRP 0.009 0.001 TRP F 330 HIS 0.013 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00588 (22218) covalent geometry : angle 0.62497 (30257) SS BOND : bond 0.00406 ( 45) SS BOND : angle 1.59046 ( 90) hydrogen bonds : bond 0.03683 ( 766) hydrogen bonds : angle 4.95017 ( 2133) link_NAG-ASN : bond 0.00242 ( 12) link_NAG-ASN : angle 2.32287 ( 36) *********************** 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 241 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.941 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: 0.8887 (pm20) cc_final: 0.8519 (pm20) REVERT: A 372 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (ttpp) REVERT: A 407 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7553 (t60) REVERT: C 160 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8492 (mmmt) REVERT: C 264 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8690 (pp20) REVERT: D 129 LYS cc_start: 0.9368 (tttm) cc_final: 0.8913 (tptm) REVERT: D 337 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8709 (mtt90) REVERT: F 71 HIS cc_start: 0.8579 (p-80) cc_final: 0.8349 (p-80) REVERT: G 78 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7168 (mt-10) REVERT: G 86 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7733 (mt-10) REVERT: H 86 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7816 (mt-10) REVERT: I 9 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7259 (mm-30) outliers start: 41 outliers final: 19 residues processed: 224 average time/residue: 0.6460 time to fit residues: 165.3978 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 : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 372 LYS 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 126 THR 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 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 278 ILE 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 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 135 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 274 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** D 225 GLN D 341 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 = 0.3299 r_free = 0.3299 target = 0.095589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.064220 restraints weight = 46717.318| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.01 r_work: 0.2516 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22275 Z= 0.148 Angle : 0.580 10.402 30383 Z= 0.292 Chirality : 0.046 0.271 3463 Planarity : 0.003 0.036 3860 Dihedral : 5.788 57.850 3242 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.20 % Rotamer: Outliers : 1.34 % Allowed : 10.11 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2750 helix: 1.83 (0.28), residues: 315 sheet: -0.01 (0.17), residues: 1002 loop : -0.60 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 303 TYR 0.016 0.001 TYR E 308 PHE 0.015 0.001 PHE F 134 TRP 0.009 0.001 TRP C 89 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00340 (22218) covalent geometry : angle 0.57259 (30257) SS BOND : bond 0.00260 ( 45) SS BOND : angle 1.25488 ( 90) hydrogen bonds : bond 0.03322 ( 766) hydrogen bonds : angle 4.74748 ( 2133) link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 2.02724 ( 36) *********************** 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 237 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.853 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: 0.8863 (pm20) cc_final: 0.8512 (pm20) REVERT: A 407 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7565 (t60) REVERT: C 160 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8506 (mmmt) REVERT: C 264 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8805 (pp20) REVERT: C 327 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.5532 (p-80) REVERT: D 129 LYS cc_start: 0.9361 (tttm) cc_final: 0.8894 (tptm) REVERT: F 71 HIS cc_start: 0.8586 (p-80) cc_final: 0.8346 (p-80) REVERT: G 2 LEU cc_start: 0.6443 (mm) cc_final: 0.5995 (mt) REVERT: G 78 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7101 (mt-10) REVERT: H 78 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7095 (mt-10) REVERT: H 86 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7780 (mt-10) REVERT: I 9 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7230 (mm-30) outliers start: 32 outliers final: 16 residues processed: 226 average time/residue: 0.6170 time to fit residues: 159.7609 Evaluate side-chains 211 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 SER 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 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 D residue 374 VAL Chi-restraints excluded: chain E residue 220 ARG 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 51 GLU Chi-restraints excluded: chain I residue 11 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 223 optimal weight: 0.0570 chunk 54 optimal weight: 8.9990 chunk 268 optimal weight: 30.0000 chunk 160 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 GLN E 364 ASN F 341 GLN H 76 HIS ** 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 = 0.3259 r_free = 0.3259 target = 0.093574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.062196 restraints weight = 46821.213| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 2.99 r_work: 0.2460 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22275 Z= 0.275 Angle : 0.633 10.266 30383 Z= 0.320 Chirality : 0.048 0.280 3463 Planarity : 0.004 0.040 3860 Dihedral : 5.862 57.591 3242 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 2.10 % Allowed : 10.62 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2750 helix: 1.81 (0.29), residues: 311 sheet: -0.03 (0.17), residues: 995 loop : -0.56 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 303 TYR 0.022 0.001 TYR E 308 PHE 0.022 0.001 PHE F 134 TRP 0.007 0.001 TRP B 351 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00643 (22218) covalent geometry : angle 0.62314 (30257) SS BOND : bond 0.00436 ( 45) SS BOND : angle 1.59811 ( 90) hydrogen bonds : bond 0.03560 ( 766) hydrogen bonds : angle 4.79467 ( 2133) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.28993 ( 36) *********************** 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 249 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8848 (pm20) cc_final: 0.8507 (pm20) REVERT: A 230 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8487 (p-80) REVERT: A 407 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7591 (t60) REVERT: C 160 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8499 (mmmt) REVERT: C 264 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8656 (pp20) REVERT: D 337 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8710 (mtt90) REVERT: F 71 HIS cc_start: 0.8548 (p-80) cc_final: 0.8329 (p-80) REVERT: G 78 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7162 (mt-10) REVERT: H 78 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7034 (mt-10) REVERT: H 86 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7724 (mt-10) REVERT: I 9 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 50 outliers final: 26 residues processed: 233 average time/residue: 0.6091 time to fit residues: 162.4235 Evaluate side-chains 219 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 SER 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 365 VAL Chi-restraints excluded: chain C residue 19 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 372 LYS 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 219 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 156 optimal weight: 10.0000 chunk 260 optimal weight: 0.0470 chunk 128 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 73 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 GLN D 363 HIS E 364 ASN E 396 GLN I 3 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.066324 restraints weight = 46424.849| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.94 r_work: 0.2558 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22275 Z= 0.104 Angle : 0.562 9.570 30383 Z= 0.282 Chirality : 0.045 0.259 3463 Planarity : 0.003 0.035 3860 Dihedral : 5.427 58.074 3242 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.47 % Allowed : 12.13 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2750 helix: 2.01 (0.28), residues: 315 sheet: -0.12 (0.16), residues: 1025 loop : -0.51 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 303 TYR 0.011 0.001 TYR E 308 PHE 0.027 0.001 PHE F 134 TRP 0.012 0.001 TRP C 89 HIS 0.005 0.000 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00228 (22218) covalent geometry : angle 0.55722 (30257) SS BOND : bond 0.00247 ( 45) SS BOND : angle 0.98417 ( 90) hydrogen bonds : bond 0.03061 ( 766) hydrogen bonds : angle 4.55081 ( 2133) link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 1.77094 ( 36) *********************** 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 243 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7596 (t60) REVERT: C 160 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8460 (mmmt) REVERT: C 264 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8825 (pp20) REVERT: D 239 ASN cc_start: 0.8764 (p0) cc_final: 0.8554 (p0) REVERT: F 71 HIS cc_start: 0.8560 (p-80) cc_final: 0.8331 (p-80) REVERT: G 78 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7172 (mt-10) REVERT: H 78 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7125 (mt-10) REVERT: H 86 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7800 (mt-10) REVERT: I 9 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7216 (mm-30) outliers start: 35 outliers final: 15 residues processed: 231 average time/residue: 0.6327 time to fit residues: 167.1248 Evaluate side-chains 210 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 372 LYS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain G residue 46 LEU 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 200 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 GLN D 225 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 = 0.3256 r_free = 0.3256 target = 0.093195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.061600 restraints weight = 46914.274| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.03 r_work: 0.2452 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 22275 Z= 0.308 Angle : 0.657 10.020 30383 Z= 0.330 Chirality : 0.049 0.285 3463 Planarity : 0.004 0.045 3860 Dihedral : 5.786 57.870 3242 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 1.93 % Allowed : 12.55 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2750 helix: 1.94 (0.29), residues: 311 sheet: -0.02 (0.17), residues: 998 loop : -0.55 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 303 TYR 0.024 0.001 TYR E 308 PHE 0.040 0.002 PHE F 134 TRP 0.010 0.001 TRP B 351 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00719 (22218) covalent geometry : angle 0.64692 (30257) SS BOND : bond 0.00507 ( 45) SS BOND : angle 1.67369 ( 90) hydrogen bonds : bond 0.03569 ( 766) hydrogen bonds : angle 4.74746 ( 2133) link_NAG-ASN : bond 0.00321 ( 12) link_NAG-ASN : angle 2.26034 ( 36) *********************** 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 235 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.7620 (t60) REVERT: C 160 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8502 (mmmt) REVERT: C 264 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8652 (pp20) REVERT: D 337 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8738 (mtt90) REVERT: F 20 ARG cc_start: 0.8730 (ppt170) cc_final: 0.8473 (ptm-80) REVERT: F 71 HIS cc_start: 0.8549 (p-80) cc_final: 0.8340 (p-80) REVERT: G 2 LEU cc_start: 0.6544 (mm) cc_final: 0.6280 (mt) REVERT: G 78 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7078 (mt-10) REVERT: H 78 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7005 (mt-10) REVERT: I 9 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7079 (mm-30) outliers start: 46 outliers final: 26 residues processed: 218 average time/residue: 0.6274 time to fit residues: 156.8154 Evaluate side-chains 213 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 54 VAL Chi-restraints excluded: chain C residue 100 ASN 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 407 TRP 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 63 CYS Chi-restraints excluded: chain E residue 124 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 270 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** D 71 HIS E 364 ASN E 396 GLN H 76 HIS ** 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 = 0.3265 r_free = 0.3265 target = 0.093717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.063145 restraints weight = 46937.427| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.91 r_work: 0.2475 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22275 Z= 0.241 Angle : 0.631 9.748 30383 Z= 0.316 Chirality : 0.047 0.276 3463 Planarity : 0.004 0.047 3860 Dihedral : 5.731 57.268 3242 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 1.76 % Allowed : 13.18 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.16), residues: 2750 helix: 1.97 (0.29), residues: 311 sheet: -0.12 (0.16), residues: 1048 loop : -0.60 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 303 TYR 0.020 0.001 TYR E 308 PHE 0.034 0.001 PHE F 134 TRP 0.008 0.001 TRP B 351 HIS 0.008 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00560 (22218) covalent geometry : angle 0.62298 (30257) SS BOND : bond 0.00393 ( 45) SS BOND : angle 1.45692 ( 90) hydrogen bonds : bond 0.03426 ( 766) hydrogen bonds : angle 4.71422 ( 2133) link_NAG-ASN : bond 0.00216 ( 12) link_NAG-ASN : angle 2.15111 ( 36) *********************** 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 234 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.767 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: 0.8792 (OUTLIER) cc_final: 0.8536 (p-80) REVERT: A 407 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.7605 (t60) REVERT: C 160 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8482 (mmmt) REVERT: C 264 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8625 (pp20) REVERT: F 20 ARG cc_start: 0.8707 (ppt170) cc_final: 0.8440 (ptm-80) REVERT: F 71 HIS cc_start: 0.8526 (p-80) cc_final: 0.8306 (p-80) REVERT: G 2 LEU cc_start: 0.6536 (mm) cc_final: 0.6281 (mt) REVERT: G 78 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7189 (mt-10) REVERT: H 78 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7055 (mt-10) REVERT: I 9 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7126 (mm-30) outliers start: 42 outliers final: 27 residues processed: 221 average time/residue: 0.5869 time to fit residues: 148.9011 Evaluate side-chains 215 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 54 VAL Chi-restraints excluded: chain C residue 100 ASN 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 71 HIS Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 63 CYS 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 G residue 23 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU 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 68 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.095533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.064361 restraints weight = 46552.497| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.99 r_work: 0.2509 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22275 Z= 0.125 Angle : 0.598 9.559 30383 Z= 0.298 Chirality : 0.046 0.268 3463 Planarity : 0.003 0.051 3860 Dihedral : 5.523 57.312 3242 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 1.26 % Allowed : 13.93 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2750 helix: 2.01 (0.29), residues: 311 sheet: -0.11 (0.17), residues: 1010 loop : -0.55 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 303 TYR 0.014 0.001 TYR E 308 PHE 0.021 0.001 PHE F 134 TRP 0.012 0.001 TRP A 89 HIS 0.011 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00285 (22218) covalent geometry : angle 0.59267 (30257) SS BOND : bond 0.00233 ( 45) SS BOND : angle 1.12997 ( 90) hydrogen bonds : bond 0.03131 ( 766) hydrogen bonds : angle 4.58031 ( 2133) link_NAG-ASN : bond 0.00186 ( 12) link_NAG-ASN : angle 1.88639 ( 36) *********************** 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 220 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.880 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: 0.8685 (OUTLIER) cc_final: 0.8449 (p-80) REVERT: A 407 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.7616 (t60) REVERT: C 160 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8499 (mmmt) REVERT: C 264 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8658 (pp20) REVERT: F 20 ARG cc_start: 0.8705 (ppt170) cc_final: 0.8443 (ptm-80) REVERT: F 71 HIS cc_start: 0.8478 (p-80) cc_final: 0.8257 (p-80) REVERT: G 78 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7068 (mt-10) REVERT: H 78 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6942 (mt-10) REVERT: I 9 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7106 (mm-30) outliers start: 30 outliers final: 17 residues processed: 208 average time/residue: 0.5785 time to fit residues: 138.2132 Evaluate side-chains 204 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 365 VAL 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 413 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 323 ASP Chi-restraints excluded: chain G residue 23 LEU 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 103 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 235 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 327 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.064604 restraints weight = 46672.487| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.01 r_work: 0.2522 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2182 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= 0.135 Angle : 0.597 10.056 30383 Z= 0.296 Chirality : 0.046 0.265 3463 Planarity : 0.003 0.053 3860 Dihedral : 5.428 57.301 3242 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.44 % Favored : 95.45 % Rotamer: Outliers : 1.05 % Allowed : 14.18 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2750 helix: 2.02 (0.29), residues: 311 sheet: -0.06 (0.17), residues: 1008 loop : -0.52 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 303 TYR 0.015 0.001 TYR E 308 PHE 0.021 0.001 PHE F 134 TRP 0.011 0.001 TRP C 89 HIS 0.010 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00313 (22218) covalent geometry : angle 0.59200 (30257) SS BOND : bond 0.00259 ( 45) SS BOND : angle 1.12806 ( 90) hydrogen bonds : bond 0.03080 ( 766) hydrogen bonds : angle 4.52815 ( 2133) link_NAG-ASN : bond 0.00197 ( 12) link_NAG-ASN : angle 1.81947 ( 36) ********************** 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 218 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.751 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: 0.8390 (OUTLIER) cc_final: 0.7580 (t60) REVERT: C 24 TYR cc_start: 0.8735 (m-80) cc_final: 0.8528 (m-80) REVERT: C 160 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8514 (mmmt) REVERT: C 264 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8671 (pp20) REVERT: D 239 ASN cc_start: 0.8866 (p0) cc_final: 0.8602 (p0) REVERT: F 20 ARG cc_start: 0.8704 (ppt170) cc_final: 0.8432 (ptm-80) REVERT: F 71 HIS cc_start: 0.8495 (p-80) cc_final: 0.8278 (p-80) REVERT: G 78 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7069 (mt-10) REVERT: H 78 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6906 (mt-10) REVERT: I 9 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7092 (mm-30) outliers start: 25 outliers final: 17 residues processed: 210 average time/residue: 0.6042 time to fit residues: 145.5622 Evaluate side-chains 205 residues out of total 2383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 303 VAL Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 365 VAL 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 413 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 323 ASP 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 239 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.095954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.064775 restraints weight = 46695.412| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.99 r_work: 0.2519 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2174 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= 0.140 Angle : 0.599 10.059 30383 Z= 0.297 Chirality : 0.045 0.263 3463 Planarity : 0.004 0.065 3860 Dihedral : 5.403 57.225 3242 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 1.01 % Allowed : 14.56 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2750 helix: 2.04 (0.29), residues: 311 sheet: -0.06 (0.17), residues: 1008 loop : -0.50 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 303 TYR 0.015 0.001 TYR E 308 PHE 0.021 0.001 PHE F 134 TRP 0.010 0.001 TRP C 89 HIS 0.010 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00326 (22218) covalent geometry : angle 0.59360 (30257) SS BOND : bond 0.00247 ( 45) SS BOND : angle 1.10680 ( 90) hydrogen bonds : bond 0.03069 ( 766) hydrogen bonds : angle 4.48245 ( 2133) link_NAG-ASN : bond 0.00187 ( 12) link_NAG-ASN : angle 1.79745 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8307.45 seconds wall clock time: 142 minutes 11.66 seconds (8531.66 seconds total)