Starting phenix.real_space_refine on Mon May 19 20:34:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gav_29909/05_2025/8gav_29909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gav_29909/05_2025/8gav_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_29909/05_2025/8gav_29909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gav_29909/05_2025/8gav_29909.map" model { file = "/net/cci-nas-00/data/ceres_data/8gav_29909/05_2025/8gav_29909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gav_29909/05_2025/8gav_29909.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "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 Chain: "C" 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: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 789 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Restraints were copied for chains: B, E, I, F, H, J, G, K, L Time building chain proxies: 8.72, per 1000 atoms: 0.46 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=36, 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 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 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: 4.57 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.09 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: 6.78 Time building geometry restraints manager: 5.38 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: 608 28.58 - 42.87: 116 42.87 - 57.16: 44 57.16 - 71.45: 8 Dihedral angle restraints: 11712 sinusoidal: 4736 harmonic: 6976 Sorted by residual: 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 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 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 11709 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: 2.04 - 2.61: 132 2.61 - 3.18: 14544 3.18 - 3.75: 27072 3.75 - 4.33: 39548 4.33 - 4.90: 68440 Nonbonded interactions: 149736 Sorted by model distance: nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " model vdw 2.037 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " model vdw 2.044 3.760 ... (remaining 149731 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' selection = chain 'L' } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 42.230 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.800 ------------------------------------------------------------------------------- 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 19568 Z= 0.458 Angle : 1.061 11.171 26588 Z= 0.586 Chirality : 0.069 0.219 2904 Planarity : 0.008 0.063 3408 Dihedral : 9.776 71.448 7180 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.041 0.005 TRP B 115 HIS 0.022 0.004 HIS A 310 PHE 0.064 0.008 PHE A 205 TYR 0.041 0.005 TYR D 32 ARG 0.019 0.002 ARG I 85 Details of bonding type rmsd link_NAG-ASN : bond 0.01450 ( 12) link_NAG-ASN : angle 3.34365 ( 36) hydrogen bonds : bond 0.25595 ( 540) hydrogen bonds : angle 10.20639 ( 1560) SS BOND : bond 0.00576 ( 36) SS BOND : angle 2.19282 ( 72) covalent geometry : bond 0.01073 (19520) covalent geometry : angle 1.04990 (26480) *********************** 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 : 2.321 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: 0.7540 (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: 0.8168 (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: 0.8337 (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: 0.8219 (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: 0.7722 (tt0) REVERT: F 89 VAL cc_start: 0.8481 (t) cc_final: 0.8143 (p) REVERT: I 88 SER cc_start: 0.8264 (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: 0.8475 (t) cc_final: 0.8152 (p) outliers start: 8 outliers final: 9 residues processed: 495 average time/residue: 1.1740 time to fit residues: 659.8904 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 : 2.061 ------------------------------------------------------------------------------- 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 202 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.114243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100419 restraints weight = 24421.671| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.48 r_work: 0.3177 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19568 Z= 0.145 Angle : 0.618 6.109 26588 Z= 0.331 Chirality : 0.048 0.153 2904 Planarity : 0.005 0.054 3408 Dihedral : 6.875 55.469 2950 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.27 % Allowed : 6.82 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2440 helix: -2.95 (0.55), residues: 24 sheet: -0.69 (0.16), residues: 988 loop : -2.04 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 115 HIS 0.004 0.001 HIS B 310 PHE 0.018 0.003 PHE E 410 TYR 0.016 0.002 TYR L 32 ARG 0.007 0.000 ARG E 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.13493 ( 36) hydrogen bonds : bond 0.04263 ( 540) hydrogen bonds : angle 6.35627 ( 1560) SS BOND : bond 0.00175 ( 36) SS BOND : angle 0.96221 ( 72) covalent geometry : bond 0.00333 (19520) covalent geometry : angle 0.61204 (26480) *********************** 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: 48 poor density : 441 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8084 (t0) cc_final: 0.7811 (t0) REVERT: A 425 GLU cc_start: 0.8169 (tt0) cc_final: 0.7822 (tt0) REVERT: A 431 LYS cc_start: 0.8175 (tppt) cc_final: 0.7945 (tppt) REVERT: A 432 GLU cc_start: 0.7744 (mp0) cc_final: 0.7443 (mp0) REVERT: H 89 VAL cc_start: 0.8543 (t) cc_final: 0.8219 (p) REVERT: B 234 ASN cc_start: 0.8184 (t0) cc_final: 0.7804 (t0) REVERT: B 432 GLU cc_start: 0.7722 (mp0) cc_final: 0.7325 (mp0) REVERT: C 89 VAL cc_start: 0.8566 (t) cc_final: 0.8246 (p) REVERT: E 385 ASN cc_start: 0.8229 (t0) cc_final: 0.8007 (t0) REVERT: E 425 GLU cc_start: 0.8231 (tt0) cc_final: 0.7941 (tt0) REVERT: F 82 MET cc_start: 0.8167 (mtp) cc_final: 0.7958 (mtp) REVERT: F 89 VAL cc_start: 0.8553 (t) cc_final: 0.8273 (p) REVERT: I 271 SER cc_start: 0.8806 (p) cc_final: 0.8602 (m) REVERT: I 425 GLU cc_start: 0.8189 (tt0) cc_final: 0.7891 (tt0) REVERT: J 89 VAL cc_start: 0.8539 (t) cc_final: 0.8271 (p) outliers start: 48 outliers final: 21 residues processed: 461 average time/residue: 1.1263 time to fit residues: 592.8046 Evaluate side-chains 417 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 396 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 128 LYS 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 128 LYS 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 228 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099346 restraints weight = 24190.586| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.47 r_work: 0.3165 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19568 Z= 0.161 Angle : 0.621 6.234 26588 Z= 0.330 Chirality : 0.047 0.154 2904 Planarity : 0.005 0.053 3408 Dihedral : 6.083 39.898 2940 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.60 % Allowed : 10.56 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2440 helix: -2.23 (0.74), residues: 24 sheet: -0.07 (0.17), residues: 916 loop : -1.89 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 178 HIS 0.005 0.001 HIS A 336 PHE 0.021 0.003 PHE A 205 TYR 0.015 0.002 TYR E 155 ARG 0.004 0.000 ARG I 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 12) link_NAG-ASN : angle 2.49133 ( 36) hydrogen bonds : bond 0.04111 ( 540) hydrogen bonds : angle 5.77798 ( 1560) SS BOND : bond 0.00242 ( 36) SS BOND : angle 1.49527 ( 72) covalent geometry : bond 0.00383 (19520) covalent geometry : angle 0.61044 (26480) *********************** 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 463 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 408 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (mmm160) REVERT: A 234 ASN cc_start: 0.8116 (t0) cc_final: 0.7829 (t0) REVERT: A 425 GLU cc_start: 0.8181 (tt0) cc_final: 0.7844 (tt0) REVERT: A 431 LYS cc_start: 0.8075 (tppt) cc_final: 0.7810 (tppt) REVERT: A 432 GLU cc_start: 0.7715 (mp0) cc_final: 0.7411 (mp0) REVERT: H 89 VAL cc_start: 0.8554 (t) cc_final: 0.8243 (p) REVERT: B 234 ASN cc_start: 0.8217 (t0) cc_final: 0.7823 (t0) REVERT: B 432 GLU cc_start: 0.7738 (mp0) cc_final: 0.7319 (mp0) REVERT: C 89 VAL cc_start: 0.8539 (t) cc_final: 0.8250 (p) REVERT: E 385 ASN cc_start: 0.8344 (t0) cc_final: 0.8107 (t0) REVERT: E 391 GLN cc_start: 0.8359 (pt0) cc_final: 0.8139 (pt0) REVERT: F 89 VAL cc_start: 0.8563 (t) cc_final: 0.8304 (p) REVERT: I 140 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8317 (tp) REVERT: I 425 GLU cc_start: 0.8242 (tt0) cc_final: 0.7923 (tt0) REVERT: J 82 MET cc_start: 0.8204 (mtp) cc_final: 0.7956 (mtp) REVERT: J 82 ASN cc_start: 0.8330 (m-40) cc_final: 0.7934 (m-40) REVERT: J 89 VAL cc_start: 0.8500 (t) cc_final: 0.8271 (p) outliers start: 55 outliers final: 29 residues processed: 437 average time/residue: 1.1923 time to fit residues: 594.2858 Evaluate side-chains 423 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 392 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 309 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER 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 390 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS 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 332 SER 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 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 99 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 175 optimal weight: 0.0020 chunk 192 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 0.0050 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- 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 226 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 = 0.3506 r_free = 0.3506 target = 0.115445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101152 restraints weight = 24225.567| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.54 r_work: 0.3191 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19568 Z= 0.095 Angle : 0.543 7.475 26588 Z= 0.287 Chirality : 0.045 0.151 2904 Planarity : 0.004 0.047 3408 Dihedral : 5.416 35.540 2940 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.56 % Allowed : 12.41 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.16), residues: 2440 helix: -1.93 (0.76), residues: 24 sheet: 0.01 (0.17), residues: 928 loop : -1.63 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.003 0.001 HIS I 336 PHE 0.013 0.002 PHE A 410 TYR 0.011 0.001 TYR H 91 ARG 0.004 0.000 ARG I 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 2.06516 ( 36) hydrogen bonds : bond 0.03164 ( 540) hydrogen bonds : angle 5.34513 ( 1560) SS BOND : bond 0.00111 ( 36) SS BOND : angle 1.33202 ( 72) covalent geometry : bond 0.00216 (19520) covalent geometry : angle 0.53463 (26480) *********************** 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 474 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 420 time to evaluate : 2.202 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: 0.8225 (OUTLIER) cc_final: 0.7900 (mmm160) REVERT: A 431 LYS cc_start: 0.8058 (tppt) cc_final: 0.7800 (tppt) REVERT: A 432 GLU cc_start: 0.7694 (mp0) cc_final: 0.7418 (mp0) REVERT: H 89 VAL cc_start: 0.8485 (t) cc_final: 0.8205 (p) REVERT: B 234 ASN cc_start: 0.8186 (t0) cc_final: 0.7793 (t0) REVERT: B 247 THR cc_start: 0.8304 (p) cc_final: 0.8085 (t) REVERT: B 432 GLU cc_start: 0.7729 (mp0) cc_final: 0.7333 (mp0) REVERT: C 82 ASN cc_start: 0.8462 (m-40) cc_final: 0.8145 (m-40) REVERT: E 425 GLU cc_start: 0.8170 (tt0) cc_final: 0.7778 (tt0) REVERT: E 432 GLU cc_start: 0.7743 (mp0) cc_final: 0.7397 (mp0) REVERT: F 82 MET cc_start: 0.8110 (mtp) cc_final: 0.7882 (mtp) REVERT: F 82 ASN cc_start: 0.8369 (m-40) cc_final: 0.8017 (m-40) REVERT: F 89 VAL cc_start: 0.8468 (t) cc_final: 0.8224 (p) REVERT: I 313 VAL cc_start: 0.8747 (m) cc_final: 0.8520 (t) REVERT: I 425 GLU cc_start: 0.8148 (tt0) cc_final: 0.7834 (tt0) REVERT: I 431 LYS cc_start: 0.8115 (tppt) cc_final: 0.7888 (mppt) REVERT: J 82 ASN cc_start: 0.8335 (m-40) cc_final: 0.7982 (m-40) REVERT: J 89 VAL cc_start: 0.8459 (t) cc_final: 0.8225 (p) outliers start: 54 outliers final: 30 residues processed: 450 average time/residue: 1.2517 time to fit residues: 634.9504 Evaluate side-chains 428 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 397 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 309 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 399 ASP 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 L residue 27 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 G residue 27 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain J residue 62 SER 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 93 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 226 GLN E 294 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097439 restraints weight = 24364.153| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.47 r_work: 0.3133 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19568 Z= 0.249 Angle : 0.700 7.686 26588 Z= 0.365 Chirality : 0.050 0.150 2904 Planarity : 0.005 0.067 3408 Dihedral : 6.006 37.815 2940 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.84 % Allowed : 13.78 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2440 helix: -2.12 (0.75), residues: 24 sheet: 0.42 (0.17), residues: 900 loop : -1.65 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 178 HIS 0.007 0.002 HIS E 310 PHE 0.032 0.004 PHE B 205 TYR 0.022 0.003 TYR E 130 ARG 0.007 0.001 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 12) link_NAG-ASN : angle 2.93798 ( 36) hydrogen bonds : bond 0.04372 ( 540) hydrogen bonds : angle 5.55804 ( 1560) SS BOND : bond 0.00371 ( 36) SS BOND : angle 2.23152 ( 72) covalent geometry : bond 0.00603 (19520) covalent geometry : angle 0.68312 (26480) *********************** 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 466 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 2.123 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: 0.8329 (OUTLIER) cc_final: 0.8092 (mmm160) REVERT: A 234 ASN cc_start: 0.8142 (t0) cc_final: 0.7845 (t0) REVERT: A 425 GLU cc_start: 0.8294 (tt0) cc_final: 0.7890 (tt0) REVERT: A 431 LYS cc_start: 0.8075 (tppt) cc_final: 0.7804 (tppt) REVERT: A 432 GLU cc_start: 0.7827 (mp0) cc_final: 0.7472 (mp0) REVERT: H 89 VAL cc_start: 0.8565 (t) cc_final: 0.8263 (p) REVERT: B 234 ASN cc_start: 0.8203 (t0) cc_final: 0.7831 (t0) REVERT: B 432 GLU cc_start: 0.7827 (mp0) cc_final: 0.7386 (mp0) REVERT: C 82 ASN cc_start: 0.8550 (m-40) cc_final: 0.8191 (m-40) REVERT: C 82 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8444 (mp) REVERT: C 89 VAL cc_start: 0.8541 (t) cc_final: 0.8260 (p) REVERT: E 140 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8213 (tp) REVERT: F 82 ASN cc_start: 0.8457 (m-40) cc_final: 0.8112 (m-40) REVERT: F 89 VAL cc_start: 0.8570 (t) cc_final: 0.8309 (p) REVERT: I 140 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8148 (tp) REVERT: I 313 VAL cc_start: 0.8794 (m) cc_final: 0.8584 (t) REVERT: I 425 GLU cc_start: 0.8237 (tt0) cc_final: 0.7935 (tt0) REVERT: J 82 ASN cc_start: 0.8488 (m-40) cc_final: 0.8121 (m-40) REVERT: J 89 VAL cc_start: 0.8518 (t) cc_final: 0.8290 (p) outliers start: 60 outliers final: 33 residues processed: 440 average time/residue: 1.1468 time to fit residues: 574.7464 Evaluate side-chains 439 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 402 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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 452 THR Chi-restraints excluded: chain H residue 62 SER 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 390 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 G residue 22 SER Chi-restraints excluded: chain G residue 27 THR 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 309 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 62 SER 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 204 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.112826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098232 restraints weight = 24401.782| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.58 r_work: 0.3143 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19568 Z= 0.139 Angle : 0.606 8.879 26588 Z= 0.317 Chirality : 0.046 0.149 2904 Planarity : 0.004 0.053 3408 Dihedral : 5.578 38.075 2940 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.75 % Allowed : 14.63 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2440 helix: -2.05 (0.76), residues: 24 sheet: 0.33 (0.17), residues: 920 loop : -1.54 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 178 HIS 0.003 0.001 HIS E 310 PHE 0.017 0.002 PHE A 410 TYR 0.015 0.001 TYR H 91 ARG 0.005 0.000 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.55929 ( 36) hydrogen bonds : bond 0.03537 ( 540) hydrogen bonds : angle 5.33424 ( 1560) SS BOND : bond 0.00374 ( 36) SS BOND : angle 2.12945 ( 72) covalent geometry : bond 0.00330 (19520) covalent geometry : angle 0.58997 (26480) *********************** 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 469 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 411 time to evaluate : 2.313 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: 0.8323 (OUTLIER) cc_final: 0.8061 (mmm160) REVERT: A 234 ASN cc_start: 0.8116 (t0) cc_final: 0.7788 (t0) REVERT: A 431 LYS cc_start: 0.8058 (tppt) cc_final: 0.7805 (tppt) REVERT: A 432 GLU cc_start: 0.7894 (mp0) cc_final: 0.7528 (mp0) REVERT: H 82 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (mp) REVERT: H 89 VAL cc_start: 0.8519 (t) cc_final: 0.8229 (p) REVERT: L 22 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 234 ASN cc_start: 0.8211 (t0) cc_final: 0.7820 (t0) REVERT: B 338 LEU cc_start: 0.8006 (mt) cc_final: 0.7759 (mp) REVERT: B 432 GLU cc_start: 0.7879 (mp0) cc_final: 0.7444 (mp0) REVERT: C 82 ASN cc_start: 0.8501 (m-40) cc_final: 0.8191 (m-40) REVERT: C 89 VAL cc_start: 0.8505 (t) cc_final: 0.8195 (p) REVERT: F 82 ASN cc_start: 0.8437 (m-40) cc_final: 0.8076 (m-40) REVERT: F 89 VAL cc_start: 0.8488 (t) cc_final: 0.8221 (p) REVERT: I 140 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (tp) REVERT: I 313 VAL cc_start: 0.8723 (m) cc_final: 0.8513 (t) REVERT: I 425 GLU cc_start: 0.8195 (tt0) cc_final: 0.7908 (tt0) REVERT: J 82 ASN cc_start: 0.8430 (m-40) cc_final: 0.8088 (m-40) REVERT: J 89 VAL cc_start: 0.8478 (t) cc_final: 0.8251 (p) outliers start: 58 outliers final: 36 residues processed: 441 average time/residue: 1.1678 time to fit residues: 584.9825 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 404 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 294 ASN 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 82 LEU 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 215 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 242 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 91 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 309 ASP Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 chunk 133 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 226 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 = 0.3484 r_free = 0.3484 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101785 restraints weight = 24455.972| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.48 r_work: 0.3160 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19568 Z= 0.125 Angle : 0.593 10.830 26588 Z= 0.309 Chirality : 0.046 0.145 2904 Planarity : 0.004 0.055 3408 Dihedral : 5.401 38.036 2940 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.56 % Allowed : 15.29 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2440 helix: -1.93 (0.78), residues: 24 sheet: 0.45 (0.17), residues: 920 loop : -1.43 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 178 HIS 0.004 0.001 HIS A 336 PHE 0.016 0.002 PHE A 410 TYR 0.016 0.001 TYR H 91 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 12) link_NAG-ASN : angle 2.49118 ( 36) hydrogen bonds : bond 0.03309 ( 540) hydrogen bonds : angle 5.20324 ( 1560) SS BOND : bond 0.00500 ( 36) SS BOND : angle 2.34508 ( 72) covalent geometry : bond 0.00294 (19520) covalent geometry : angle 0.57390 (26480) *********************** 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 464 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 410 time to evaluate : 2.330 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: 0.8289 (OUTLIER) cc_final: 0.7983 (mmm160) REVERT: A 234 ASN cc_start: 0.8066 (t0) cc_final: 0.7746 (t0) REVERT: A 431 LYS cc_start: 0.8048 (tppt) cc_final: 0.7799 (tppt) REVERT: A 432 GLU cc_start: 0.7829 (mp0) cc_final: 0.7497 (mp0) REVERT: H 89 VAL cc_start: 0.8519 (t) cc_final: 0.8236 (p) REVERT: B 234 ASN cc_start: 0.8141 (t0) cc_final: 0.7756 (t0) REVERT: B 338 LEU cc_start: 0.8003 (mt) cc_final: 0.7767 (mp) REVERT: B 432 GLU cc_start: 0.7866 (mp0) cc_final: 0.7432 (mp0) REVERT: C 82 ASN cc_start: 0.8489 (m-40) cc_final: 0.8204 (m-40) REVERT: C 89 VAL cc_start: 0.8459 (t) cc_final: 0.8156 (p) REVERT: D 46 LEU cc_start: 0.8546 (tp) cc_final: 0.8333 (tt) REVERT: E 425 GLU cc_start: 0.8158 (tt0) cc_final: 0.7905 (tt0) REVERT: F 82 ASN cc_start: 0.8465 (m-40) cc_final: 0.8107 (m-40) REVERT: F 89 VAL cc_start: 0.8466 (t) cc_final: 0.8192 (p) REVERT: I 313 VAL cc_start: 0.8731 (m) cc_final: 0.8514 (t) REVERT: I 425 GLU cc_start: 0.8128 (tt0) cc_final: 0.7821 (tt0) REVERT: J 82 ASN cc_start: 0.8437 (m-40) cc_final: 0.8096 (m-40) REVERT: J 89 VAL cc_start: 0.8442 (t) cc_final: 0.8227 (p) outliers start: 54 outliers final: 41 residues processed: 437 average time/residue: 1.1934 time to fit residues: 590.7414 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 294 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR 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 215 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 242 THR 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 399 ASP 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 G residue 91 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 370 SER 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 K residue 12 SER 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 91 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 168 optimal weight: 0.0670 chunk 185 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.115249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101015 restraints weight = 24511.053| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.48 r_work: 0.3148 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19568 Z= 0.165 Angle : 0.626 12.855 26588 Z= 0.326 Chirality : 0.047 0.147 2904 Planarity : 0.005 0.058 3408 Dihedral : 5.497 37.751 2940 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.65 % Allowed : 15.62 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2440 helix: -1.98 (0.76), residues: 24 sheet: 0.63 (0.17), residues: 896 loop : -1.38 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 178 HIS 0.006 0.001 HIS A 336 PHE 0.019 0.002 PHE B 205 TYR 0.018 0.002 TYR H 91 ARG 0.005 0.000 ARG I 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.67590 ( 36) hydrogen bonds : bond 0.03578 ( 540) hydrogen bonds : angle 5.25104 ( 1560) SS BOND : bond 0.00452 ( 36) SS BOND : angle 2.32990 ( 72) covalent geometry : bond 0.00397 (19520) covalent geometry : angle 0.60755 (26480) *********************** 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 458 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 2.075 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: 0.8059 (mmm160) REVERT: A 234 ASN cc_start: 0.8079 (t0) cc_final: 0.7775 (t0) REVERT: A 431 LYS cc_start: 0.8038 (tppt) cc_final: 0.7814 (tppt) REVERT: A 432 GLU cc_start: 0.7849 (mp0) cc_final: 0.7495 (mp0) REVERT: H 89 VAL cc_start: 0.8502 (t) cc_final: 0.8212 (p) REVERT: B 234 ASN cc_start: 0.8182 (t0) cc_final: 0.7803 (t0) REVERT: B 338 LEU cc_start: 0.8102 (mt) cc_final: 0.7882 (mp) REVERT: B 432 GLU cc_start: 0.7893 (mp0) cc_final: 0.7461 (mp0) REVERT: C 82 ASN cc_start: 0.8499 (m-40) cc_final: 0.8206 (m-40) REVERT: C 89 VAL cc_start: 0.8466 (t) cc_final: 0.8171 (p) REVERT: E 140 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8117 (tp) REVERT: F 82 ASN cc_start: 0.8472 (m-40) cc_final: 0.8118 (m-40) REVERT: F 89 VAL cc_start: 0.8502 (t) cc_final: 0.8228 (p) REVERT: I 140 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8147 (tp) REVERT: I 313 VAL cc_start: 0.8740 (m) cc_final: 0.8524 (t) REVERT: I 425 GLU cc_start: 0.8171 (tt0) cc_final: 0.7877 (tt0) REVERT: J 82 ASN cc_start: 0.8460 (m-40) cc_final: 0.8119 (m-40) REVERT: J 89 VAL cc_start: 0.8440 (t) cc_final: 0.8221 (p) outliers start: 56 outliers final: 44 residues processed: 427 average time/residue: 1.1650 time to fit residues: 563.3878 Evaluate side-chains 442 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 395 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP 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 L residue 95 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 242 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP 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 G residue 22 SER 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 G residue 91 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 370 SER Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain K residue 12 SER 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 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.115683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101400 restraints weight = 24402.126| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.49 r_work: 0.3155 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19568 Z= 0.146 Angle : 0.639 15.276 26588 Z= 0.330 Chirality : 0.047 0.242 2904 Planarity : 0.004 0.056 3408 Dihedral : 5.506 37.269 2940 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.65 % Allowed : 15.62 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.16), residues: 2440 helix: -1.98 (0.77), residues: 24 sheet: 0.53 (0.17), residues: 912 loop : -1.37 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 178 HIS 0.010 0.001 HIS A 336 PHE 0.018 0.002 PHE A 410 TYR 0.017 0.001 TYR H 91 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.63460 ( 36) hydrogen bonds : bond 0.03445 ( 540) hydrogen bonds : angle 5.21620 ( 1560) SS BOND : bond 0.00548 ( 36) SS BOND : angle 2.50017 ( 72) covalent geometry : bond 0.00348 (19520) covalent geometry : angle 0.61919 (26480) *********************** 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 458 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 1.990 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: 0.8297 (OUTLIER) cc_final: 0.8024 (mmm160) REVERT: A 234 ASN cc_start: 0.8070 (t0) cc_final: 0.7762 (t0) REVERT: A 431 LYS cc_start: 0.8029 (tppt) cc_final: 0.7803 (tppt) REVERT: A 432 GLU cc_start: 0.7848 (mp0) cc_final: 0.7496 (mp0) REVERT: H 89 VAL cc_start: 0.8489 (t) cc_final: 0.8205 (p) REVERT: B 234 ASN cc_start: 0.8188 (t0) cc_final: 0.7785 (t0) REVERT: B 247 THR cc_start: 0.8354 (p) cc_final: 0.8142 (t) REVERT: B 432 GLU cc_start: 0.7876 (mp0) cc_final: 0.7449 (mp0) REVERT: C 82 ASN cc_start: 0.8494 (m-40) cc_final: 0.8193 (m-40) REVERT: C 82 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8410 (mp) REVERT: C 89 VAL cc_start: 0.8465 (t) cc_final: 0.8172 (p) REVERT: E 140 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8113 (tp) REVERT: F 82 ASN cc_start: 0.8469 (m-40) cc_final: 0.8117 (m-40) REVERT: F 89 VAL cc_start: 0.8495 (t) cc_final: 0.8221 (p) REVERT: I 140 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8134 (tp) REVERT: I 313 VAL cc_start: 0.8714 (m) cc_final: 0.8511 (t) REVERT: I 425 GLU cc_start: 0.8157 (tt0) cc_final: 0.7874 (tt0) REVERT: J 82 ASN cc_start: 0.8437 (m-40) cc_final: 0.8088 (m-40) REVERT: J 89 VAL cc_start: 0.8466 (t) cc_final: 0.8246 (p) outliers start: 56 outliers final: 45 residues processed: 431 average time/residue: 1.2029 time to fit residues: 586.8312 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 395 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP 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 L residue 48 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 242 THR 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 399 ASP Chi-restraints excluded: chain G residue 22 SER 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 G residue 91 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 370 SER 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 K residue 12 SER 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 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.0570 chunk 20 optimal weight: 0.2980 chunk 157 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 194 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102752 restraints weight = 24371.509| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.48 r_work: 0.3186 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19568 Z= 0.105 Angle : 0.591 15.785 26588 Z= 0.305 Chirality : 0.046 0.258 2904 Planarity : 0.004 0.053 3408 Dihedral : 5.306 36.243 2940 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.18 % Allowed : 16.15 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2440 helix: -1.84 (0.79), residues: 24 sheet: 0.54 (0.17), residues: 920 loop : -1.28 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 178 HIS 0.004 0.001 HIS E 336 PHE 0.015 0.002 PHE A 410 TYR 0.016 0.001 TYR H 91 ARG 0.005 0.000 ARG I 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 2.35910 ( 36) hydrogen bonds : bond 0.03032 ( 540) hydrogen bonds : angle 5.08858 ( 1560) SS BOND : bond 0.00345 ( 36) SS BOND : angle 2.08885 ( 72) covalent geometry : bond 0.00242 (19520) covalent geometry : angle 0.57537 (26480) ********************** 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 465 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 2.173 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: 0.8250 (OUTLIER) cc_final: 0.7958 (mmm160) REVERT: A 306 ASN cc_start: 0.8434 (t0) cc_final: 0.8142 (t0) REVERT: A 391 GLN cc_start: 0.8460 (pt0) cc_final: 0.8161 (pt0) REVERT: A 431 LYS cc_start: 0.8020 (tppt) cc_final: 0.7781 (tppt) REVERT: A 432 GLU cc_start: 0.7835 (mp0) cc_final: 0.7496 (mp0) REVERT: H 89 VAL cc_start: 0.8489 (t) cc_final: 0.8223 (p) REVERT: B 234 ASN cc_start: 0.8184 (t0) cc_final: 0.7757 (t0) REVERT: B 432 GLU cc_start: 0.7876 (mp0) cc_final: 0.7434 (mp0) REVERT: C 82 ASN cc_start: 0.8449 (m-40) cc_final: 0.8193 (m-40) REVERT: E 140 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8118 (tp) REVERT: F 82 ASN cc_start: 0.8455 (m-40) cc_final: 0.8119 (m-40) REVERT: F 89 VAL cc_start: 0.8429 (t) cc_final: 0.8178 (p) REVERT: I 140 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8101 (tp) REVERT: J 82 ASN cc_start: 0.8394 (m-40) cc_final: 0.8065 (m-40) REVERT: J 89 VAL cc_start: 0.8405 (t) cc_final: 0.8195 (p) outliers start: 46 outliers final: 37 residues processed: 441 average time/residue: 1.2374 time to fit residues: 618.2082 Evaluate side-chains 449 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 409 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP 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 95 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE 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 242 THR 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 G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 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 K residue 12 SER 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 139 optimal weight: 1.9990 chunk 221 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 245 ASN L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 245 ASN E 294 ASN G 37 GLN I 245 ASN I 294 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099343 restraints weight = 24558.955| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.57 r_work: 0.3117 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19568 Z= 0.252 Angle : 0.735 14.570 26588 Z= 0.380 Chirality : 0.051 0.269 2904 Planarity : 0.005 0.062 3408 Dihedral : 5.885 38.724 2940 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.37 % Allowed : 16.52 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2440 helix: -2.13 (0.74), residues: 24 sheet: 0.76 (0.17), residues: 896 loop : -1.46 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 178 HIS 0.008 0.002 HIS A 336 PHE 0.030 0.003 PHE B 205 TYR 0.021 0.002 TYR H 91 ARG 0.005 0.001 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 12) link_NAG-ASN : angle 3.09023 ( 36) hydrogen bonds : bond 0.04167 ( 540) hydrogen bonds : angle 5.41979 ( 1560) SS BOND : bond 0.00440 ( 36) SS BOND : angle 2.65166 ( 72) covalent geometry : bond 0.00614 (19520) covalent geometry : angle 0.71457 (26480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14065.17 seconds wall clock time: 242 minutes 37.14 seconds (14557.14 seconds total)