Starting phenix.real_space_refine on Thu Mar 5 03:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.map" model { file = "/net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gav_29909/03_2026/8gav_29909.cif" } resolution = 2.7 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= 0.001 sd= 0.025 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 120 5.16 5 C 11860 2.51 5 N 3320 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3000 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 373} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 789 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, E, I, C, F, J, D, G, K Time building chain proxies: 3.46, per 1000 atoms: 0.18 Number of scatterers: 19088 At special positions: 0 Unit cell: (132.09, 132.09, 96.57, 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 120 16.00 O 3788 8.00 N 3320 7.00 C 11860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS E 175 " - pdb=" SG CYS E 193 " distance=2.02 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 291 " distance=2.04 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.04 Simple disulfide: pdb=" SG CYS E 421 " - pdb=" SG CYS E 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 146 " " NAG A 502 " - " ASN A 200 " " NAG A 503 " - " ASN A 367 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 200 " " NAG B 503 " - " ASN B 367 " " NAG E 501 " - " ASN E 146 " " NAG E 502 " - " ASN E 200 " " NAG E 503 " - " ASN E 367 " " NAG I 501 " - " ASN I 146 " " NAG I 502 " - " ASN I 200 " " NAG I 503 " - " ASN I 367 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 840.9 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 56 sheets defined 3.6% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER B 145 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER E 145 " --> pdb=" O ASN E 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 146' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER F 87 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER I 145 " --> pdb=" O ASN I 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 408 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A 252 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU A 372 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 400 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 376 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL A 396 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG A 394 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=10, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 93 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 93 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL L 19 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR L 95A" --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 408 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA B 133 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 236 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR B 252 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 254 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 261 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU B 372 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG B 400 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 376 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 396 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS B 378 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 394 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 428 through 429 Processing sheet with id=22, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=24, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 93 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 93 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL D 19 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 95A" --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 408 " --> pdb=" O TYR E 423 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA E 133 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS E 175 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET E 160 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN E 173 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER E 179 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP E 213 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'E' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 236 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR E 252 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE E 254 " --> pdb=" O THR E 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE E 256 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS E 261 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'E' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS E 278 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS E 280 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 311 " --> pdb=" O ASN E 306 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU E 372 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG E 400 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR E 376 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL E 396 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS E 378 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG E 394 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 428 through 429 Processing sheet with id=36, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 78 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=38, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL G 19 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR G 95A" --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY I 408 " --> pdb=" O TYR I 423 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA I 133 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS I 175 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET I 160 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN I 173 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'I' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER I 179 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'I' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL I 231 " --> pdb=" O THR I 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 236 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR I 252 " --> pdb=" O LYS I 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS I 267 " --> pdb=" O THR I 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE I 254 " --> pdb=" O THR I 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR I 265 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE I 256 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS I 261 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'I' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS I 278 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL I 290 " --> pdb=" O CYS I 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS I 280 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG I 288 " --> pdb=" O CYS I 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 311 " --> pdb=" O ASN I 306 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU I 372 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG I 400 " --> pdb=" O LEU I 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR I 376 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL I 396 " --> pdb=" O THR I 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS I 378 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG I 394 " --> pdb=" O LYS I 378 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'I' and resid 428 through 429 Processing sheet with id=50, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=52, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 93 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 93 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL K 19 " --> pdb=" O VAL K 75 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR K 95A" --> pdb=" O GLU K 92 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1560 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: 4.20 Time building geometry restraints manager: 2.17 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: 6196 1.34 - 1.46: 5052 1.46 - 1.59: 8120 1.59 - 1.71: 0 1.71 - 1.84: 152 Bond restraints: 19520 Sorted by residual: bond pdb=" CA SER K 52 " pdb=" CB SER K 52 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.39e-02 5.18e+03 1.02e+01 bond pdb=" CA SER L 52 " pdb=" CB SER L 52 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.39e-02 5.18e+03 1.02e+01 bond pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.39e-02 5.18e+03 1.02e+01 bond pdb=" CA SER G 52 " pdb=" CB SER G 52 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.39e-02 5.18e+03 1.02e+01 bond pdb=" N ASP G 50 " pdb=" CA ASP G 50 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.15e+00 ... (remaining 19515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 25200 2.23 - 4.47: 1104 4.47 - 6.70: 148 6.70 - 8.94: 20 8.94 - 11.17: 8 Bond angle restraints: 26480 Sorted by residual: angle pdb=" N THR L 27 " pdb=" CA THR L 27 " pdb=" C THR L 27 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N THR D 27 " pdb=" CA THR D 27 " pdb=" C THR D 27 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N THR K 27 " pdb=" CA THR K 27 " pdb=" C THR K 27 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N THR G 27 " pdb=" CA THR G 27 " pdb=" C THR G 27 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N TRP H 100A" pdb=" CA TRP H 100A" pdb=" C TRP H 100A" ideal model delta sigma weight residual 110.80 118.15 -7.35 2.13e+00 2.20e-01 1.19e+01 ... (remaining 26475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 10936 14.29 - 28.58: 628 28.58 - 42.87: 116 42.87 - 57.16: 48 57.16 - 71.45: 8 Dihedral angle restraints: 11736 sinusoidal: 4760 harmonic: 6976 Sorted by residual: dihedral pdb=" CA THR L 26 " pdb=" C THR L 26 " pdb=" N THR L 27 " pdb=" CA THR L 27 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA THR K 26 " pdb=" C THR K 26 " pdb=" N THR K 27 " pdb=" CA THR K 27 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA THR G 26 " pdb=" C THR G 26 " pdb=" N THR G 27 " pdb=" CA THR G 27 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1432 0.044 - 0.088: 916 0.088 - 0.131: 376 0.131 - 0.175: 132 0.175 - 0.219: 48 Chirality restraints: 2904 Sorted by residual: chirality pdb=" CB THR G 27 " pdb=" CA THR G 27 " pdb=" OG1 THR G 27 " pdb=" CG2 THR G 27 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR K 27 " pdb=" CA THR K 27 " pdb=" OG1 THR K 27 " pdb=" CG2 THR K 27 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR L 27 " pdb=" CA THR L 27 " pdb=" OG1 THR L 27 " pdb=" CG2 THR L 27 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2901 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 205 " -0.035 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A 205 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE A 205 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 205 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 205 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 205 " -0.035 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE E 205 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE E 205 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 205 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 205 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 205 " -0.035 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE I 205 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE I 205 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE I 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE I 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 205 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE I 205 " -0.008 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5508 2.82 - 3.34: 14144 3.34 - 3.86: 30780 3.86 - 4.38: 35220 4.38 - 4.90: 64060 Nonbonded interactions: 149712 Sorted by model distance: nonbonded pdb=" OE1 GLN E 136 " pdb=" NH1 ARG E 156 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLN A 136 " pdb=" NH1 ARG A 156 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLN I 136 " pdb=" NH1 ARG I 156 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLN B 136 " pdb=" NH1 ARG B 156 " model vdw 2.296 3.120 nonbonded pdb=" OG SER A 217 " pdb=" OD2 ASP A 243 " model vdw 2.302 3.040 ... (remaining 149707 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'C' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'D' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.011 0.098 19576 Z= 0.458 Angle : 1.062 11.171 26604 Z= 0.586 Chirality : 0.069 0.219 2904 Planarity : 0.008 0.063 3408 Dihedral : 9.776 71.448 7180 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.74 % Favored : 94.10 % Rotamer: Outliers : 0.38 % Allowed : 1.89 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -3.07 (0.14), residues: 2440 helix: -4.19 (0.27), residues: 24 sheet: -1.46 (0.16), residues: 932 loop : -2.48 (0.13), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG I 85 TYR 0.041 0.005 TYR D 32 PHE 0.064 0.008 PHE A 205 TRP 0.041 0.005 TRP B 115 HIS 0.022 0.004 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.01073 (19520) covalent geometry : angle 1.04990 (26480) SS BOND : bond 0.00677 ( 44) SS BOND : angle 2.17824 ( 88) hydrogen bonds : bond 0.25595 ( 540) hydrogen bonds : angle 10.20639 ( 1560) link_NAG-ASN : bond 0.01450 ( 12) link_NAG-ASN : angle 3.34365 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 487 time to evaluate : 0.766 Fit side-chains REVERT: A 92 CYS cc_start: 0.6486 (m) cc_final: 0.6259 (m) REVERT: A 126 LEU cc_start: 0.8466 (mt) cc_final: 0.8128 (mm) REVERT: A 234 ASN cc_start: 0.7539 (t0) cc_final: 0.7164 (t0) REVERT: A 271 SER cc_start: 0.8635 (p) cc_final: 0.8400 (m) REVERT: A 425 GLU cc_start: 0.7863 (tt0) cc_final: 0.7638 (tt0) REVERT: A 432 GLU cc_start: 0.7220 (mp0) cc_final: 0.6958 (mp0) REVERT: H 89 VAL cc_start: 0.8543 (t) cc_final: 0.8169 (p) REVERT: B 92 CYS cc_start: 0.6318 (m) cc_final: 0.6068 (m) REVERT: B 126 LEU cc_start: 0.8645 (mt) cc_final: 0.8336 (mm) REVERT: B 234 ASN cc_start: 0.7640 (t0) cc_final: 0.7310 (t0) REVERT: C 89 VAL cc_start: 0.8522 (t) cc_final: 0.8162 (p) REVERT: E 92 CYS cc_start: 0.6315 (m) cc_final: 0.6085 (m) REVERT: E 126 LEU cc_start: 0.8552 (mt) cc_final: 0.8220 (mm) REVERT: E 271 SER cc_start: 0.8544 (p) cc_final: 0.8330 (t) REVERT: E 425 GLU cc_start: 0.7954 (tt0) cc_final: 0.7723 (tt0) REVERT: F 89 VAL cc_start: 0.8481 (t) cc_final: 0.8143 (p) REVERT: I 88 SER cc_start: 0.8265 (p) cc_final: 0.8022 (m) REVERT: I 126 LEU cc_start: 0.8490 (mt) cc_final: 0.8154 (mm) REVERT: I 271 SER cc_start: 0.8572 (p) cc_final: 0.8244 (t) REVERT: I 425 GLU cc_start: 0.7945 (tt0) cc_final: 0.7695 (tt0) REVERT: J 89 VAL cc_start: 0.8474 (t) cc_final: 0.8152 (p) outliers start: 8 outliers final: 9 residues processed: 495 average time/residue: 0.5978 time to fit residues: 334.2109 Evaluate side-chains 420 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 411 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 50 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 235 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN L 37 GLN B 226 GLN B 294 ASN B 385 ASN C 73 ASN D 37 GLN E 226 GLN E 391 GLN G 37 GLN I 226 GLN I 294 ASN J 73 ASN K 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100171 restraints weight = 24234.590| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.53 r_work: 0.3179 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19576 Z= 0.132 Angle : 0.614 6.119 26604 Z= 0.329 Chirality : 0.047 0.152 2904 Planarity : 0.005 0.054 3408 Dihedral : 6.822 55.570 2950 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.18 % Allowed : 6.58 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: -2.14 (0.16), residues: 2440 helix: -2.97 (0.54), residues: 24 sheet: -0.67 (0.16), residues: 996 loop : -2.02 (0.14), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 156 TYR 0.014 0.002 TYR L 32 PHE 0.018 0.002 PHE A 205 TRP 0.016 0.002 TRP A 115 HIS 0.003 0.001 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00303 (19520) covalent geometry : angle 0.60680 (26480) SS BOND : bond 0.00310 ( 44) SS BOND : angle 1.24594 ( 88) hydrogen bonds : bond 0.04370 ( 540) hydrogen bonds : angle 6.34955 ( 1560) link_NAG-ASN : bond 0.00339 ( 12) link_NAG-ASN : angle 2.05885 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 443 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8091 (t0) cc_final: 0.7829 (t0) REVERT: A 425 GLU cc_start: 0.8171 (tt0) cc_final: 0.7842 (tt0) REVERT: A 431 LYS cc_start: 0.8180 (tppt) cc_final: 0.7949 (tppt) REVERT: A 432 GLU cc_start: 0.7769 (mp0) cc_final: 0.7469 (mp0) REVERT: H 89 VAL cc_start: 0.8523 (t) cc_final: 0.8193 (p) REVERT: B 234 ASN cc_start: 0.8191 (t0) cc_final: 0.7826 (t0) REVERT: B 432 GLU cc_start: 0.7757 (mp0) cc_final: 0.7342 (mp0) REVERT: C 89 VAL cc_start: 0.8540 (t) cc_final: 0.8204 (p) REVERT: E 385 ASN cc_start: 0.8227 (t0) cc_final: 0.8003 (t0) REVERT: E 425 GLU cc_start: 0.8236 (tt0) cc_final: 0.7961 (tt0) REVERT: F 82 MET cc_start: 0.8179 (mtp) cc_final: 0.7972 (mtp) REVERT: F 89 VAL cc_start: 0.8507 (t) cc_final: 0.8211 (p) REVERT: I 425 GLU cc_start: 0.8200 (tt0) cc_final: 0.7868 (tt0) REVERT: J 89 VAL cc_start: 0.8509 (t) cc_final: 0.8239 (p) outliers start: 46 outliers final: 19 residues processed: 463 average time/residue: 0.5664 time to fit residues: 297.4796 Evaluate side-chains 424 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 405 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 212 optimal weight: 0.0570 chunk 92 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 294 ASN D 37 GLN E 294 ASN E 358 ASN G 37 GLN I 226 GLN I 294 ASN I 358 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098072 restraints weight = 24434.666| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.53 r_work: 0.3150 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19576 Z= 0.192 Angle : 0.656 6.272 26604 Z= 0.348 Chirality : 0.048 0.162 2904 Planarity : 0.005 0.053 3408 Dihedral : 6.239 42.153 2940 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.32 % Allowed : 10.89 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -1.67 (0.16), residues: 2440 helix: -2.31 (0.71), residues: 24 sheet: 0.05 (0.17), residues: 908 loop : -1.95 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 38 TYR 0.018 0.002 TYR B 155 PHE 0.024 0.003 PHE B 205 TRP 0.018 0.002 TRP A 178 HIS 0.006 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00460 (19520) covalent geometry : angle 0.64224 (26480) SS BOND : bond 0.00444 ( 44) SS BOND : angle 1.71648 ( 88) hydrogen bonds : bond 0.04475 ( 540) hydrogen bonds : angle 5.83701 ( 1560) link_NAG-ASN : bond 0.00370 ( 12) link_NAG-ASN : angle 2.64757 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 412 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8032 (mmm160) REVERT: A 234 ASN cc_start: 0.8156 (t0) cc_final: 0.7885 (t0) REVERT: A 425 GLU cc_start: 0.8184 (tt0) cc_final: 0.7854 (tt0) REVERT: A 431 LYS cc_start: 0.8086 (tppt) cc_final: 0.7822 (tppt) REVERT: A 432 GLU cc_start: 0.7749 (mp0) cc_final: 0.7428 (mp0) REVERT: H 89 VAL cc_start: 0.8531 (t) cc_final: 0.8214 (p) REVERT: B 234 ASN cc_start: 0.8218 (t0) cc_final: 0.7841 (t0) REVERT: B 338 LEU cc_start: 0.8063 (mt) cc_final: 0.7846 (mp) REVERT: B 432 GLU cc_start: 0.7769 (mp0) cc_final: 0.7347 (mp0) REVERT: C 89 VAL cc_start: 0.8513 (t) cc_final: 0.8214 (p) REVERT: E 385 ASN cc_start: 0.8341 (t0) cc_final: 0.8115 (t0) REVERT: F 89 VAL cc_start: 0.8518 (t) cc_final: 0.8242 (p) REVERT: I 140 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8295 (tp) REVERT: I 425 GLU cc_start: 0.8281 (tt0) cc_final: 0.7964 (tt0) REVERT: J 82 ASN cc_start: 0.8413 (m-40) cc_final: 0.7960 (m-40) REVERT: J 89 VAL cc_start: 0.8478 (t) cc_final: 0.8248 (p) outliers start: 49 outliers final: 27 residues processed: 436 average time/residue: 0.5843 time to fit residues: 287.3779 Evaluate side-chains 424 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 395 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098445 restraints weight = 24267.368| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.48 r_work: 0.3150 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19576 Z= 0.199 Angle : 0.658 7.789 26604 Z= 0.347 Chirality : 0.049 0.154 2904 Planarity : 0.005 0.051 3408 Dihedral : 6.077 38.042 2940 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.89 % Allowed : 12.41 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -1.39 (0.16), residues: 2440 helix: -2.22 (0.72), residues: 24 sheet: 0.26 (0.17), residues: 908 loop : -1.76 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.018 0.002 TYR E 130 PHE 0.025 0.003 PHE B 205 TRP 0.021 0.002 TRP B 178 HIS 0.006 0.001 HIS I 336 Details of bonding type rmsd covalent geometry : bond 0.00479 (19520) covalent geometry : angle 0.64470 (26480) SS BOND : bond 0.00427 ( 44) SS BOND : angle 1.70318 ( 88) hydrogen bonds : bond 0.04272 ( 540) hydrogen bonds : angle 5.64898 ( 1560) link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 2.76010 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 410 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8063 (mmm160) REVERT: A 234 ASN cc_start: 0.8128 (t0) cc_final: 0.7857 (t0) REVERT: A 425 GLU cc_start: 0.8166 (tt0) cc_final: 0.7889 (tt0) REVERT: A 431 LYS cc_start: 0.8091 (tppt) cc_final: 0.7809 (tppt) REVERT: A 432 GLU cc_start: 0.7788 (mp0) cc_final: 0.7440 (mp0) REVERT: H 89 VAL cc_start: 0.8498 (t) cc_final: 0.8195 (p) REVERT: H 94 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8026 (ptt-90) REVERT: B 234 ASN cc_start: 0.8196 (t0) cc_final: 0.7821 (t0) REVERT: B 432 GLU cc_start: 0.7821 (mp0) cc_final: 0.7367 (mp0) REVERT: C 82 ASN cc_start: 0.8495 (m-40) cc_final: 0.8178 (m-40) REVERT: C 89 VAL cc_start: 0.8488 (t) cc_final: 0.8179 (p) REVERT: C 94 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7780 (ptt-90) REVERT: F 82 ASN cc_start: 0.8404 (m-40) cc_final: 0.8058 (m-40) REVERT: F 89 VAL cc_start: 0.8495 (t) cc_final: 0.8209 (p) REVERT: F 94 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7791 (ptt-90) REVERT: I 313 VAL cc_start: 0.8789 (m) cc_final: 0.8571 (t) REVERT: I 425 GLU cc_start: 0.8210 (tt0) cc_final: 0.7899 (tt0) REVERT: J 82 ASN cc_start: 0.8447 (m-40) cc_final: 0.8061 (m-40) REVERT: J 82 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8349 (mp) REVERT: J 89 VAL cc_start: 0.8459 (t) cc_final: 0.8219 (p) REVERT: J 94 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7885 (ptt-90) outliers start: 61 outliers final: 39 residues processed: 446 average time/residue: 0.5918 time to fit residues: 297.5064 Evaluate side-chains 448 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 403 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.0770 chunk 26 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099489 restraints weight = 24172.212| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.53 r_work: 0.3163 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19576 Z= 0.120 Angle : 0.586 6.938 26604 Z= 0.308 Chirality : 0.046 0.152 2904 Planarity : 0.004 0.053 3408 Dihedral : 5.572 37.373 2940 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.84 % Allowed : 13.35 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -1.12 (0.16), residues: 2440 helix: -2.07 (0.74), residues: 24 sheet: 0.41 (0.17), residues: 924 loop : -1.56 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 315 TYR 0.012 0.001 TYR B 121 PHE 0.016 0.002 PHE A 410 TRP 0.018 0.001 TRP B 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00279 (19520) covalent geometry : angle 0.57290 (26480) SS BOND : bond 0.00338 ( 44) SS BOND : angle 1.55718 ( 88) hydrogen bonds : bond 0.03577 ( 540) hydrogen bonds : angle 5.38200 ( 1560) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 2.45161 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8016 (mmm160) REVERT: A 234 ASN cc_start: 0.8088 (t0) cc_final: 0.7746 (t0) REVERT: A 425 GLU cc_start: 0.8120 (tt0) cc_final: 0.7830 (tt0) REVERT: A 431 LYS cc_start: 0.8018 (tppt) cc_final: 0.7757 (tppt) REVERT: A 432 GLU cc_start: 0.7856 (mp0) cc_final: 0.7495 (mp0) REVERT: H 89 VAL cc_start: 0.8479 (t) cc_final: 0.8178 (p) REVERT: H 94 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8073 (ptt-90) REVERT: L 46 LEU cc_start: 0.8567 (tp) cc_final: 0.8365 (tt) REVERT: B 234 ASN cc_start: 0.8183 (t0) cc_final: 0.7790 (t0) REVERT: B 432 GLU cc_start: 0.7827 (mp0) cc_final: 0.7406 (mp0) REVERT: C 82 ASN cc_start: 0.8488 (m-40) cc_final: 0.8189 (m-40) REVERT: C 89 VAL cc_start: 0.8430 (t) cc_final: 0.8135 (p) REVERT: C 94 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7908 (ptt-90) REVERT: F 82 ASN cc_start: 0.8451 (m-40) cc_final: 0.8086 (m-40) REVERT: F 89 VAL cc_start: 0.8421 (t) cc_final: 0.8163 (p) REVERT: F 94 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7923 (ptt-90) REVERT: I 313 VAL cc_start: 0.8722 (m) cc_final: 0.8501 (t) REVERT: I 425 GLU cc_start: 0.8138 (tt0) cc_final: 0.7837 (tt0) REVERT: J 82 ASN cc_start: 0.8416 (m-40) cc_final: 0.8084 (m-40) REVERT: J 89 VAL cc_start: 0.8431 (t) cc_final: 0.8201 (p) REVERT: J 94 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7917 (ptt-90) outliers start: 60 outliers final: 31 residues processed: 467 average time/residue: 0.6091 time to fit residues: 319.6167 Evaluate side-chains 454 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 418 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 157 optimal weight: 0.0060 chunk 10 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 228 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 294 ASN L 37 GLN B 245 ASN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101857 restraints weight = 24542.447| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.53 r_work: 0.3165 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19576 Z= 0.115 Angle : 0.593 12.121 26604 Z= 0.308 Chirality : 0.045 0.156 2904 Planarity : 0.004 0.054 3408 Dihedral : 5.349 37.049 2940 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.60 % Allowed : 14.58 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.91 (0.16), residues: 2440 helix: -1.83 (0.77), residues: 24 sheet: 0.55 (0.17), residues: 924 loop : -1.42 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 292 TYR 0.011 0.001 TYR B 121 PHE 0.015 0.002 PHE A 410 TRP 0.016 0.001 TRP B 178 HIS 0.003 0.001 HIS I 336 Details of bonding type rmsd covalent geometry : bond 0.00267 (19520) covalent geometry : angle 0.57095 (26480) SS BOND : bond 0.00501 ( 44) SS BOND : angle 2.45392 ( 88) hydrogen bonds : bond 0.03391 ( 540) hydrogen bonds : angle 5.22584 ( 1560) link_NAG-ASN : bond 0.00267 ( 12) link_NAG-ASN : angle 2.33100 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7989 (mmm160) REVERT: A 234 ASN cc_start: 0.8080 (t0) cc_final: 0.7762 (t0) REVERT: A 431 LYS cc_start: 0.8032 (tppt) cc_final: 0.7785 (tppt) REVERT: A 432 GLU cc_start: 0.7821 (mp0) cc_final: 0.7491 (mp0) REVERT: H 89 VAL cc_start: 0.8458 (t) cc_final: 0.8151 (p) REVERT: H 94 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8025 (ptt-90) REVERT: B 234 ASN cc_start: 0.8148 (t0) cc_final: 0.7763 (t0) REVERT: B 247 THR cc_start: 0.8336 (p) cc_final: 0.8134 (t) REVERT: B 338 LEU cc_start: 0.8045 (mt) cc_final: 0.7805 (mp) REVERT: B 432 GLU cc_start: 0.7893 (mp0) cc_final: 0.7484 (mp0) REVERT: C 82 ASN cc_start: 0.8494 (m-40) cc_final: 0.8192 (m-40) REVERT: C 94 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7904 (ptt-90) REVERT: D 46 LEU cc_start: 0.8545 (tp) cc_final: 0.8312 (tt) REVERT: F 82 ASN cc_start: 0.8470 (m-40) cc_final: 0.8105 (m-40) REVERT: F 89 VAL cc_start: 0.8384 (t) cc_final: 0.8126 (p) REVERT: F 94 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7883 (ptt-90) REVERT: I 313 VAL cc_start: 0.8723 (m) cc_final: 0.8505 (t) REVERT: I 425 GLU cc_start: 0.8112 (tt0) cc_final: 0.7783 (tt0) REVERT: J 82 ASN cc_start: 0.8418 (m-40) cc_final: 0.8099 (m-40) REVERT: J 89 VAL cc_start: 0.8389 (t) cc_final: 0.8165 (p) REVERT: J 94 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7898 (ptt-90) outliers start: 55 outliers final: 36 residues processed: 454 average time/residue: 0.6149 time to fit residues: 313.7288 Evaluate side-chains 457 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN L 37 GLN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101775 restraints weight = 24452.164| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.48 r_work: 0.3168 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19576 Z= 0.147 Angle : 0.635 12.241 26604 Z= 0.328 Chirality : 0.046 0.188 2904 Planarity : 0.004 0.058 3408 Dihedral : 5.420 37.603 2940 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.03 % Allowed : 14.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.83 (0.17), residues: 2440 helix: -1.83 (0.78), residues: 24 sheet: 0.61 (0.17), residues: 924 loop : -1.37 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 292 TYR 0.012 0.001 TYR B 281 PHE 0.017 0.002 PHE I 410 TRP 0.018 0.002 TRP B 178 HIS 0.005 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00351 (19520) covalent geometry : angle 0.61112 (26480) SS BOND : bond 0.00658 ( 44) SS BOND : angle 2.63222 ( 88) hydrogen bonds : bond 0.03589 ( 540) hydrogen bonds : angle 5.24162 ( 1560) link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 2.51995 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 422 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8018 (mmm160) REVERT: A 234 ASN cc_start: 0.8068 (t0) cc_final: 0.7758 (t0) REVERT: A 431 LYS cc_start: 0.8024 (tppt) cc_final: 0.7771 (tppt) REVERT: A 432 GLU cc_start: 0.7827 (mp0) cc_final: 0.7477 (mp0) REVERT: H 89 VAL cc_start: 0.8476 (t) cc_final: 0.8165 (p) REVERT: H 94 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7982 (ptt-90) REVERT: B 234 ASN cc_start: 0.8146 (t0) cc_final: 0.7748 (t0) REVERT: B 247 THR cc_start: 0.8345 (p) cc_final: 0.8131 (t) REVERT: B 432 GLU cc_start: 0.7907 (mp0) cc_final: 0.7464 (mp0) REVERT: C 82 ASN cc_start: 0.8492 (m-40) cc_final: 0.8197 (m-40) REVERT: C 89 VAL cc_start: 0.8397 (t) cc_final: 0.8106 (p) REVERT: C 94 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7820 (ptt-90) REVERT: D 46 LEU cc_start: 0.8545 (tp) cc_final: 0.8312 (tt) REVERT: E 140 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 425 GLU cc_start: 0.8154 (tt0) cc_final: 0.7886 (tt0) REVERT: F 82 ASN cc_start: 0.8476 (m-40) cc_final: 0.8112 (m-40) REVERT: F 89 VAL cc_start: 0.8413 (t) cc_final: 0.8153 (p) REVERT: F 94 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7865 (ptt-90) REVERT: I 140 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8130 (tp) REVERT: I 313 VAL cc_start: 0.8726 (m) cc_final: 0.8516 (t) REVERT: I 425 GLU cc_start: 0.8131 (tt0) cc_final: 0.7817 (tt0) REVERT: J 82 ASN cc_start: 0.8444 (m-40) cc_final: 0.8104 (m-40) REVERT: J 89 VAL cc_start: 0.8404 (t) cc_final: 0.8174 (p) REVERT: J 94 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7916 (ptt-90) outliers start: 64 outliers final: 44 residues processed: 461 average time/residue: 0.5953 time to fit residues: 308.9348 Evaluate side-chains 464 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 413 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 337 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 0.6980 chunk 163 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102133 restraints weight = 24443.850| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.48 r_work: 0.3167 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19576 Z= 0.129 Angle : 0.626 12.317 26604 Z= 0.322 Chirality : 0.046 0.253 2904 Planarity : 0.004 0.055 3408 Dihedral : 5.372 37.563 2940 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.75 % Allowed : 15.15 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.74 (0.17), residues: 2440 helix: -1.83 (0.79), residues: 24 sheet: 0.69 (0.18), residues: 924 loop : -1.31 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 292 TYR 0.013 0.001 TYR J 32 PHE 0.016 0.002 PHE A 410 TRP 0.017 0.001 TRP B 178 HIS 0.006 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00305 (19520) covalent geometry : angle 0.60884 (26480) SS BOND : bond 0.00505 ( 44) SS BOND : angle 2.15399 ( 88) hydrogen bonds : bond 0.03422 ( 540) hydrogen bonds : angle 5.19907 ( 1560) link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 2.46064 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 423 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8017 (mmm160) REVERT: A 234 ASN cc_start: 0.8058 (t0) cc_final: 0.7742 (t0) REVERT: A 431 LYS cc_start: 0.8017 (tppt) cc_final: 0.7784 (tppt) REVERT: A 432 GLU cc_start: 0.7821 (mp0) cc_final: 0.7490 (mp0) REVERT: H 89 VAL cc_start: 0.8461 (t) cc_final: 0.8144 (p) REVERT: H 94 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7976 (ptt-90) REVERT: B 234 ASN cc_start: 0.8172 (t0) cc_final: 0.7768 (t0) REVERT: B 247 THR cc_start: 0.8345 (p) cc_final: 0.8130 (t) REVERT: B 432 GLU cc_start: 0.7864 (mp0) cc_final: 0.7453 (mp0) REVERT: C 82 ASN cc_start: 0.8484 (m-40) cc_final: 0.8199 (m-40) REVERT: C 89 VAL cc_start: 0.8389 (t) cc_final: 0.8090 (p) REVERT: C 94 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7830 (ptt-90) REVERT: E 140 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8109 (tp) REVERT: E 435 GLU cc_start: 0.7492 (pt0) cc_final: 0.7274 (pt0) REVERT: F 82 ASN cc_start: 0.8460 (m-40) cc_final: 0.8114 (m-40) REVERT: F 89 VAL cc_start: 0.8403 (t) cc_final: 0.8136 (p) REVERT: F 94 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7861 (ptt-90) REVERT: I 313 VAL cc_start: 0.8716 (m) cc_final: 0.8508 (t) REVERT: J 82 ASN cc_start: 0.8420 (m-40) cc_final: 0.8095 (m-40) REVERT: J 89 VAL cc_start: 0.8395 (t) cc_final: 0.8165 (p) REVERT: J 94 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7913 (ptt-90) outliers start: 58 outliers final: 43 residues processed: 459 average time/residue: 0.6033 time to fit residues: 311.9847 Evaluate side-chains 462 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 413 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 238 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101617 restraints weight = 24302.202| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.52 r_work: 0.3164 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19576 Z= 0.144 Angle : 0.651 14.817 26604 Z= 0.333 Chirality : 0.047 0.250 2904 Planarity : 0.004 0.054 3408 Dihedral : 5.457 37.858 2940 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.51 % Allowed : 15.20 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.74 (0.17), residues: 2440 helix: -1.81 (0.79), residues: 24 sheet: 0.71 (0.18), residues: 924 loop : -1.33 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 292 TYR 0.016 0.001 TYR J 32 PHE 0.017 0.002 PHE B 410 TRP 0.018 0.001 TRP B 178 HIS 0.009 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00341 (19520) covalent geometry : angle 0.63352 (26480) SS BOND : bond 0.00492 ( 44) SS BOND : angle 2.16549 ( 88) hydrogen bonds : bond 0.03548 ( 540) hydrogen bonds : angle 5.21076 ( 1560) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 2.57641 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 409 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (mmm160) REVERT: A 234 ASN cc_start: 0.8073 (t0) cc_final: 0.7763 (t0) REVERT: A 391 GLN cc_start: 0.8451 (pt0) cc_final: 0.8107 (pt0) REVERT: A 431 LYS cc_start: 0.8015 (tppt) cc_final: 0.7778 (tppt) REVERT: A 432 GLU cc_start: 0.7859 (mp0) cc_final: 0.7504 (mp0) REVERT: H 89 VAL cc_start: 0.8483 (t) cc_final: 0.8173 (p) REVERT: H 94 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7919 (ptt-90) REVERT: B 234 ASN cc_start: 0.8194 (t0) cc_final: 0.7794 (t0) REVERT: B 247 THR cc_start: 0.8362 (p) cc_final: 0.8149 (t) REVERT: B 432 GLU cc_start: 0.7909 (mp0) cc_final: 0.7469 (mp0) REVERT: C 82 ASN cc_start: 0.8478 (m-40) cc_final: 0.8185 (m-40) REVERT: C 89 VAL cc_start: 0.8408 (t) cc_final: 0.8113 (p) REVERT: C 94 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7768 (ptt-90) REVERT: E 140 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8128 (tp) REVERT: F 82 ASN cc_start: 0.8475 (m-40) cc_final: 0.8119 (m-40) REVERT: F 89 VAL cc_start: 0.8424 (t) cc_final: 0.8154 (p) REVERT: F 94 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7821 (ptt-90) REVERT: I 140 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8133 (tp) REVERT: I 313 VAL cc_start: 0.8710 (m) cc_final: 0.8499 (t) REVERT: J 82 ASN cc_start: 0.8427 (m-40) cc_final: 0.8097 (m-40) REVERT: J 89 VAL cc_start: 0.8418 (t) cc_final: 0.8189 (p) REVERT: J 94 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7855 (ptt-90) outliers start: 53 outliers final: 42 residues processed: 439 average time/residue: 0.5997 time to fit residues: 296.8900 Evaluate side-chains 457 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 408 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 233 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 245 ASN I 294 ASN K 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100171 restraints weight = 24660.403| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.62 r_work: 0.3140 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19576 Z= 0.149 Angle : 0.671 14.880 26604 Z= 0.342 Chirality : 0.047 0.231 2904 Planarity : 0.004 0.056 3408 Dihedral : 5.496 37.912 2940 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.65 % Allowed : 15.72 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.79 (0.17), residues: 2440 helix: -1.86 (0.79), residues: 24 sheet: 0.73 (0.18), residues: 896 loop : -1.37 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 292 TYR 0.016 0.001 TYR J 32 PHE 0.018 0.002 PHE A 410 TRP 0.019 0.002 TRP B 178 HIS 0.005 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00353 (19520) covalent geometry : angle 0.65224 (26480) SS BOND : bond 0.00512 ( 44) SS BOND : angle 2.33422 ( 88) hydrogen bonds : bond 0.03571 ( 540) hydrogen bonds : angle 5.23119 ( 1560) link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 2.62952 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8019 (mmm160) REVERT: A 234 ASN cc_start: 0.8107 (t0) cc_final: 0.7786 (t0) REVERT: A 391 GLN cc_start: 0.8442 (pt0) cc_final: 0.8083 (pt0) REVERT: A 431 LYS cc_start: 0.8015 (tppt) cc_final: 0.7782 (tppt) REVERT: A 432 GLU cc_start: 0.7944 (mp0) cc_final: 0.7593 (mp0) REVERT: H 89 VAL cc_start: 0.8451 (t) cc_final: 0.8150 (p) REVERT: H 94 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: B 234 ASN cc_start: 0.8247 (t0) cc_final: 0.7813 (t0) REVERT: B 247 THR cc_start: 0.8396 (p) cc_final: 0.8182 (t) REVERT: B 432 GLU cc_start: 0.7918 (mp0) cc_final: 0.7487 (mp0) REVERT: C 82 ASN cc_start: 0.8483 (m-40) cc_final: 0.8188 (m-40) REVERT: C 89 VAL cc_start: 0.8416 (t) cc_final: 0.8126 (p) REVERT: C 94 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7854 (ptt-90) REVERT: E 140 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8101 (tp) REVERT: F 82 ASN cc_start: 0.8461 (m-40) cc_final: 0.8117 (m-40) REVERT: F 89 VAL cc_start: 0.8436 (t) cc_final: 0.8172 (p) REVERT: F 94 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: I 140 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (tp) REVERT: I 313 VAL cc_start: 0.8719 (m) cc_final: 0.8507 (t) REVERT: J 82 ASN cc_start: 0.8435 (m-40) cc_final: 0.8110 (m-40) REVERT: J 89 VAL cc_start: 0.8418 (t) cc_final: 0.8189 (p) REVERT: J 94 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7891 (ptt-90) outliers start: 56 outliers final: 46 residues processed: 437 average time/residue: 0.6186 time to fit residues: 303.8670 Evaluate side-chains 456 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 403 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 77 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 188 optimal weight: 0.3980 chunk 124 optimal weight: 0.2980 chunk 192 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN L 37 GLN B 294 ASN D 37 GLN E 245 ASN E 294 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100650 restraints weight = 24685.712| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.62 r_work: 0.3144 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19576 Z= 0.132 Angle : 0.650 13.940 26604 Z= 0.331 Chirality : 0.047 0.235 2904 Planarity : 0.004 0.050 3408 Dihedral : 5.433 37.836 2940 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.65 % Allowed : 15.72 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % 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 are not related in a simple way. whole: -0.69 (0.17), residues: 2440 helix: -1.83 (0.80), residues: 24 sheet: 0.76 (0.18), residues: 924 loop : -1.30 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 292 TYR 0.016 0.001 TYR J 32 PHE 0.018 0.002 PHE A 410 TRP 0.018 0.001 TRP B 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00311 (19520) covalent geometry : angle 0.63289 (26480) SS BOND : bond 0.00427 ( 44) SS BOND : angle 2.13039 ( 88) hydrogen bonds : bond 0.03444 ( 540) hydrogen bonds : angle 5.19299 ( 1560) link_NAG-ASN : bond 0.00261 ( 12) link_NAG-ASN : angle 2.57469 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6998.22 seconds wall clock time: 119 minutes 59.73 seconds (7199.73 seconds total)