Starting phenix.real_space_refine on Mon Jun 16 18:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gav_29909/06_2025/8gav_29909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gav_29909/06_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_29909/06_2025/8gav_29909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gav_29909/06_2025/8gav_29909.map" model { file = "/net/cci-nas-00/data/ceres_data/8gav_29909/06_2025/8gav_29909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gav_29909/06_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-5710/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: 8.56, per 1000 atoms: 0.45 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: 4.28 Conformation dependent library (CDL) restraints added in 2.3 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: 3.16 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: 6.56 Time building geometry restraints manager: 5.15 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: 0.15 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 41.830 Find NCS groups from input model: 0.400 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.980 ------------------------------------------------------------------------------- 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 : 2.031 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: 1.2165 time to fit residues: 681.0593 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 : 2.172 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100417 restraints weight = 24421.671| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.49 r_work: 0.3179 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8091 (t0) cc_final: 0.7825 (t0) REVERT: A 425 GLU cc_start: 0.8167 (tt0) cc_final: 0.7822 (tt0) REVERT: A 431 LYS cc_start: 0.8182 (tppt) cc_final: 0.7951 (tppt) REVERT: A 432 GLU cc_start: 0.7747 (mp0) cc_final: 0.7442 (mp0) REVERT: H 89 VAL cc_start: 0.8545 (t) cc_final: 0.8218 (p) REVERT: B 234 ASN cc_start: 0.8194 (t0) cc_final: 0.7813 (t0) REVERT: B 432 GLU cc_start: 0.7737 (mp0) cc_final: 0.7337 (mp0) REVERT: C 89 VAL cc_start: 0.8564 (t) cc_final: 0.8241 (p) REVERT: E 385 ASN cc_start: 0.8226 (t0) cc_final: 0.8002 (t0) REVERT: E 425 GLU cc_start: 0.8235 (tt0) cc_final: 0.7941 (tt0) REVERT: F 82 MET cc_start: 0.8169 (mtp) cc_final: 0.7960 (mtp) REVERT: F 89 VAL cc_start: 0.8551 (t) cc_final: 0.8272 (p) REVERT: I 271 SER cc_start: 0.8799 (p) cc_final: 0.8595 (m) REVERT: I 425 GLU cc_start: 0.8190 (tt0) cc_final: 0.7892 (tt0) REVERT: J 89 VAL cc_start: 0.8537 (t) cc_final: 0.8268 (p) outliers start: 48 outliers final: 21 residues processed: 461 average time/residue: 1.2006 time to fit residues: 629.7452 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 : 2.292 ------------------------------------------------------------------------------- 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: 0.3980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 221 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 294 ASN I 358 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100414 restraints weight = 24190.573| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.53 r_work: 0.3179 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19568 Z= 0.115 Angle : 0.569 6.246 26588 Z= 0.304 Chirality : 0.046 0.155 2904 Planarity : 0.005 0.049 3408 Dihedral : 5.779 34.992 2940 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.41 % Allowed : 10.56 % Favored : 87.03 % 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: -1.64 (0.16), residues: 2440 helix: -2.20 (0.73), residues: 24 sheet: -0.06 (0.17), residues: 916 loop : -1.83 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 178 HIS 0.003 0.001 HIS A 310 PHE 0.016 0.002 PHE A 205 TYR 0.013 0.001 TYR E 121 ARG 0.004 0.000 ARG I 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 12) link_NAG-ASN : angle 2.18564 ( 36) hydrogen bonds : bond 0.03652 ( 540) hydrogen bonds : angle 5.64644 ( 1560) SS BOND : bond 0.00218 ( 36) SS BOND : angle 1.05413 ( 72) covalent geometry : bond 0.00265 (19520) covalent geometry : angle 0.56223 (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 467 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 416 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7959 (mmm160) REVERT: A 234 ASN cc_start: 0.8146 (t0) cc_final: 0.7847 (t0) REVERT: A 343 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 425 GLU cc_start: 0.8127 (tt0) cc_final: 0.7820 (tt0) REVERT: A 431 LYS cc_start: 0.8087 (tppt) cc_final: 0.7817 (tppt) REVERT: A 432 GLU cc_start: 0.7709 (mp0) cc_final: 0.7405 (mp0) REVERT: H 89 VAL cc_start: 0.8514 (t) cc_final: 0.8209 (p) REVERT: B 234 ASN cc_start: 0.8236 (t0) cc_final: 0.7837 (t0) REVERT: B 432 GLU cc_start: 0.7736 (mp0) cc_final: 0.7350 (mp0) REVERT: B 435 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6525 (tm-30) REVERT: C 89 VAL cc_start: 0.8508 (t) cc_final: 0.8225 (p) REVERT: E 385 ASN cc_start: 0.8336 (t0) cc_final: 0.8086 (t0) REVERT: E 391 GLN cc_start: 0.8351 (pt0) cc_final: 0.8142 (pt0) REVERT: E 425 GLU cc_start: 0.8194 (tt0) cc_final: 0.7810 (tt0) REVERT: F 89 VAL cc_start: 0.8516 (t) cc_final: 0.8257 (p) REVERT: I 425 GLU cc_start: 0.8187 (tt0) cc_final: 0.7848 (tt0) REVERT: I 431 LYS cc_start: 0.8106 (tppt) cc_final: 0.7856 (mppt) REVERT: J 82 MET cc_start: 0.8169 (mtp) cc_final: 0.7957 (mtp) REVERT: J 82 ASN cc_start: 0.8306 (m-40) cc_final: 0.7982 (m-40) REVERT: J 89 VAL cc_start: 0.8450 (t) cc_final: 0.8226 (p) outliers start: 51 outliers final: 22 residues processed: 442 average time/residue: 1.5253 time to fit residues: 769.5817 Evaluate side-chains 413 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 390 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 L residue 27 THR 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 B residue 443 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS 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 I residue 148 THR 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: 2.9990 chunk 108 optimal weight: 0.0070 chunk 175 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 98 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.115858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101640 restraints weight = 24254.317| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.53 r_work: 0.3197 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19568 Z= 0.093 Angle : 0.534 6.786 26588 Z= 0.282 Chirality : 0.045 0.149 2904 Planarity : 0.004 0.046 3408 Dihedral : 5.295 34.817 2940 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.41 % Allowed : 12.12 % Favored : 85.46 % 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: -1.34 (0.16), residues: 2440 helix: -1.88 (0.76), residues: 24 sheet: 0.04 (0.17), residues: 956 loop : -1.59 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.006 0.001 HIS A 336 PHE 0.013 0.002 PHE A 410 TYR 0.011 0.001 TYR H 91 ARG 0.004 0.000 ARG A 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 1.98971 ( 36) hydrogen bonds : bond 0.03093 ( 540) hydrogen bonds : angle 5.27946 ( 1560) SS BOND : bond 0.00123 ( 36) SS BOND : angle 1.31911 ( 72) covalent geometry : bond 0.00212 (19520) covalent geometry : angle 0.52577 (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: 51 poor density : 423 time to evaluate : 2.188 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: 0.8211 (OUTLIER) cc_final: 0.7889 (mmm160) REVERT: A 431 LYS cc_start: 0.8055 (tppt) cc_final: 0.7799 (tppt) REVERT: A 432 GLU cc_start: 0.7685 (mp0) cc_final: 0.7405 (mp0) REVERT: H 89 VAL cc_start: 0.8460 (t) cc_final: 0.8184 (p) REVERT: B 234 ASN cc_start: 0.8194 (t0) cc_final: 0.7810 (t0) REVERT: B 247 THR cc_start: 0.8264 (p) cc_final: 0.8041 (t) REVERT: B 432 GLU cc_start: 0.7718 (mp0) cc_final: 0.7329 (mp0) REVERT: C 82 ASN cc_start: 0.8470 (m-40) cc_final: 0.8153 (m-40) REVERT: E 425 GLU cc_start: 0.8125 (tt0) cc_final: 0.7760 (tt0) REVERT: F 82 MET cc_start: 0.8097 (mtp) cc_final: 0.7874 (mtp) REVERT: F 82 ASN cc_start: 0.8363 (m-40) cc_final: 0.8017 (m-40) REVERT: F 89 VAL cc_start: 0.8462 (t) cc_final: 0.8216 (p) REVERT: I 425 GLU cc_start: 0.8131 (tt0) cc_final: 0.7793 (tt0) REVERT: J 82 ASN cc_start: 0.8336 (m-40) cc_final: 0.7996 (m-40) REVERT: J 89 VAL cc_start: 0.8443 (t) cc_final: 0.8206 (p) outliers start: 51 outliers final: 30 residues processed: 450 average time/residue: 1.3341 time to fit residues: 674.3216 Evaluate side-chains 433 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 402 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR 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 B residue 399 ASP Chi-restraints excluded: chain B residue 443 ILE 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 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 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 325 THR Chi-restraints excluded: chain I residue 399 ASP 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: 2.9990 chunk 120 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 226 GLN L 37 GLN B 245 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098888 restraints weight = 24340.099| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.52 r_work: 0.3156 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19568 Z= 0.184 Angle : 0.632 7.847 26588 Z= 0.330 Chirality : 0.047 0.213 2904 Planarity : 0.005 0.050 3408 Dihedral : 5.606 36.417 2940 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 13.78 % Favored : 83.62 % 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: -1.16 (0.16), residues: 2440 helix: -1.84 (0.79), residues: 24 sheet: 0.37 (0.17), residues: 908 loop : -1.57 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 178 HIS 0.007 0.001 HIS A 336 PHE 0.023 0.003 PHE B 205 TYR 0.017 0.002 TYR H 91 ARG 0.007 0.001 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.55575 ( 36) hydrogen bonds : bond 0.03802 ( 540) hydrogen bonds : angle 5.33162 ( 1560) SS BOND : bond 0.00301 ( 36) SS BOND : angle 1.96683 ( 72) covalent geometry : bond 0.00444 (19520) covalent geometry : angle 0.61807 (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 461 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 406 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8043 (mmm160) REVERT: A 234 ASN cc_start: 0.8122 (t0) cc_final: 0.7820 (t0) REVERT: A 425 GLU cc_start: 0.8207 (tt0) cc_final: 0.7882 (tt0) REVERT: A 431 LYS cc_start: 0.8046 (tppt) cc_final: 0.7798 (tppt) REVERT: A 432 GLU cc_start: 0.7796 (mp0) cc_final: 0.7478 (mp0) REVERT: H 89 VAL cc_start: 0.8541 (t) cc_final: 0.8273 (p) REVERT: B 234 ASN cc_start: 0.8205 (t0) cc_final: 0.7824 (t0) REVERT: B 432 GLU cc_start: 0.7778 (mp0) cc_final: 0.7361 (mp0) REVERT: C 82 ASN cc_start: 0.8522 (m-40) cc_final: 0.8208 (m-40) REVERT: C 82 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 89 VAL cc_start: 0.8485 (t) cc_final: 0.8222 (p) REVERT: E 140 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8122 (tp) REVERT: F 82 ASN cc_start: 0.8423 (m-40) cc_final: 0.8079 (m-40) REVERT: F 89 VAL cc_start: 0.8525 (t) cc_final: 0.8275 (p) REVERT: I 140 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8215 (tp) REVERT: I 313 VAL cc_start: 0.8764 (m) cc_final: 0.8542 (t) REVERT: I 425 GLU cc_start: 0.8212 (tt0) cc_final: 0.7910 (tt0) REVERT: J 82 ASN cc_start: 0.8453 (m-40) cc_final: 0.8112 (m-40) REVERT: J 89 VAL cc_start: 0.8475 (t) cc_final: 0.8271 (p) outliers start: 55 outliers final: 37 residues processed: 432 average time/residue: 1.2176 time to fit residues: 594.4712 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 403 time to evaluate : 2.011 ------------------------------------------------------------------------------- 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 370 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 390 LEU 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 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL 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 380 VAL Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain G residue 27 THR 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 I residue 380 VAL Chi-restraints excluded: chain J residue 53 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: 0.9980 chunk 190 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 237 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.113668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099366 restraints weight = 24410.749| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.50 r_work: 0.3167 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19568 Z= 0.129 Angle : 0.590 10.479 26588 Z= 0.307 Chirality : 0.046 0.156 2904 Planarity : 0.004 0.050 3408 Dihedral : 5.380 36.174 2940 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.60 % Allowed : 14.16 % Favored : 83.24 % 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: -1.06 (0.16), residues: 2440 helix: -1.86 (0.78), residues: 24 sheet: 0.40 (0.17), residues: 912 loop : -1.47 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.003 0.001 HIS I 336 PHE 0.016 0.002 PHE A 410 TYR 0.015 0.001 TYR H 91 ARG 0.006 0.000 ARG E 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 12) link_NAG-ASN : angle 2.36866 ( 36) hydrogen bonds : bond 0.03365 ( 540) hydrogen bonds : angle 5.20545 ( 1560) SS BOND : bond 0.00307 ( 36) SS BOND : angle 1.99816 ( 72) covalent geometry : bond 0.00305 (19520) covalent geometry : angle 0.57514 (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 467 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 412 time to evaluate : 4.053 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: 0.8285 (OUTLIER) cc_final: 0.7991 (mmm160) REVERT: A 234 ASN cc_start: 0.8058 (t0) cc_final: 0.7743 (t0) REVERT: A 431 LYS cc_start: 0.8013 (tppt) cc_final: 0.7772 (tppt) REVERT: A 432 GLU cc_start: 0.7838 (mp0) cc_final: 0.7501 (mp0) REVERT: H 89 VAL cc_start: 0.8499 (t) cc_final: 0.8231 (p) REVERT: B 234 ASN cc_start: 0.8217 (t0) cc_final: 0.7839 (t0) REVERT: B 432 GLU cc_start: 0.7787 (mp0) cc_final: 0.7380 (mp0) REVERT: C 82 ASN cc_start: 0.8484 (m-40) cc_final: 0.8195 (m-40) REVERT: C 89 VAL cc_start: 0.8454 (t) cc_final: 0.8177 (p) REVERT: E 140 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (tp) REVERT: F 82 ASN cc_start: 0.8440 (m-40) cc_final: 0.8081 (m-40) REVERT: F 89 VAL cc_start: 0.8480 (t) cc_final: 0.8219 (p) REVERT: G 46 LEU cc_start: 0.8643 (tp) cc_final: 0.8442 (tt) REVERT: I 140 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8167 (tp) REVERT: I 313 VAL cc_start: 0.8707 (m) cc_final: 0.8481 (t) REVERT: I 425 GLU cc_start: 0.8160 (tt0) cc_final: 0.7829 (tt0) REVERT: I 431 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7721 (mppt) REVERT: I 432 GLU cc_start: 0.7804 (mp0) cc_final: 0.7497 (mp0) REVERT: J 82 ASN cc_start: 0.8424 (m-40) cc_final: 0.8091 (m-40) REVERT: J 89 VAL cc_start: 0.8472 (t) cc_final: 0.8253 (p) outliers start: 55 outliers final: 45 residues processed: 441 average time/residue: 1.3177 time to fit residues: 658.4551 Evaluate side-chains 452 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 403 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 380 VAL 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 B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 443 ILE 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 380 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 460 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 380 VAL Chi-restraints excluded: chain I residue 399 ASP Chi-restraints excluded: chain I residue 431 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.111972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097419 restraints weight = 24218.802| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.57 r_work: 0.3132 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 19568 Z= 0.213 Angle : 0.672 11.541 26588 Z= 0.348 Chirality : 0.049 0.155 2904 Planarity : 0.005 0.052 3408 Dihedral : 5.693 37.699 2940 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.84 % Allowed : 14.49 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.16), residues: 2440 helix: -2.01 (0.76), residues: 24 sheet: 0.61 (0.17), residues: 900 loop : -1.51 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 178 HIS 0.007 0.001 HIS A 336 PHE 0.027 0.003 PHE B 205 TYR 0.019 0.002 TYR H 91 ARG 0.006 0.001 ARG I 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.82444 ( 36) hydrogen bonds : bond 0.03971 ( 540) hydrogen bonds : angle 5.36376 ( 1560) SS BOND : bond 0.00453 ( 36) SS BOND : angle 2.50827 ( 72) covalent geometry : bond 0.00516 (19520) covalent geometry : angle 0.65201 (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 460 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 400 time to evaluate : 2.610 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: 0.8337 (OUTLIER) cc_final: 0.8078 (mmm160) REVERT: A 234 ASN cc_start: 0.8120 (t0) cc_final: 0.7820 (t0) REVERT: A 431 LYS cc_start: 0.8050 (tppt) cc_final: 0.7797 (tppt) REVERT: A 432 GLU cc_start: 0.7939 (mp0) cc_final: 0.7573 (mp0) REVERT: H 89 VAL cc_start: 0.8529 (t) cc_final: 0.8236 (p) REVERT: L 22 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 234 ASN cc_start: 0.8265 (t0) cc_final: 0.7877 (t0) REVERT: B 338 LEU cc_start: 0.8052 (mt) cc_final: 0.7797 (mp) REVERT: B 432 GLU cc_start: 0.7882 (mp0) cc_final: 0.7441 (mp0) REVERT: C 82 ASN cc_start: 0.8522 (m-40) cc_final: 0.8228 (m-40) REVERT: C 89 VAL cc_start: 0.8503 (t) cc_final: 0.8199 (p) REVERT: E 140 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8128 (tp) REVERT: F 82 ASN cc_start: 0.8492 (m-40) cc_final: 0.8123 (m-40) REVERT: F 89 VAL cc_start: 0.8511 (t) cc_final: 0.8249 (p) REVERT: I 140 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8167 (tp) REVERT: I 313 VAL cc_start: 0.8737 (m) cc_final: 0.8521 (t) REVERT: I 425 GLU cc_start: 0.8253 (tt0) cc_final: 0.7939 (tt0) REVERT: J 82 ASN cc_start: 0.8484 (m-40) cc_final: 0.8143 (m-40) REVERT: J 89 VAL cc_start: 0.8520 (t) cc_final: 0.8270 (p) outliers start: 60 outliers final: 39 residues processed: 433 average time/residue: 1.6188 time to fit residues: 798.7366 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 380 VAL 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 22 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 309 ASP Chi-restraints excluded: chain B residue 370 SER 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 380 VAL 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 309 ASP 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 J residue 53 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 0.0970 chunk 217 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 0.0870 chunk 185 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.115160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100939 restraints weight = 24498.429| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.48 r_work: 0.3146 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19568 Z= 0.167 Angle : 0.637 8.958 26588 Z= 0.331 Chirality : 0.047 0.217 2904 Planarity : 0.004 0.050 3408 Dihedral : 5.575 37.501 2940 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.75 % Allowed : 14.73 % Favored : 82.53 % 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: -0.94 (0.16), residues: 2440 helix: -2.05 (0.75), residues: 24 sheet: 0.49 (0.17), residues: 924 loop : -1.41 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 178 HIS 0.005 0.001 HIS A 336 PHE 0.019 0.002 PHE B 205 TYR 0.017 0.002 TYR H 91 ARG 0.005 0.000 ARG I 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 2.70440 ( 36) hydrogen bonds : bond 0.03647 ( 540) hydrogen bonds : angle 5.30513 ( 1560) SS BOND : bond 0.00434 ( 36) SS BOND : angle 2.08687 ( 72) covalent geometry : bond 0.00402 (19520) covalent geometry : angle 0.62110 (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 465 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 407 time to evaluate : 2.167 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: 0.8330 (OUTLIER) cc_final: 0.8063 (mmm160) REVERT: A 234 ASN cc_start: 0.8088 (t0) cc_final: 0.7781 (t0) REVERT: A 431 LYS cc_start: 0.8038 (tppt) cc_final: 0.7814 (tppt) REVERT: A 432 GLU cc_start: 0.7894 (mp0) cc_final: 0.7530 (mp0) REVERT: H 89 VAL cc_start: 0.8511 (t) cc_final: 0.8223 (p) REVERT: L 22 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 234 ASN cc_start: 0.8191 (t0) cc_final: 0.7791 (t0) REVERT: B 432 GLU cc_start: 0.7909 (mp0) cc_final: 0.7483 (mp0) REVERT: C 82 ASN cc_start: 0.8486 (m-40) cc_final: 0.8174 (m-40) REVERT: C 82 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 89 VAL cc_start: 0.8472 (t) cc_final: 0.8178 (p) REVERT: E 140 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8154 (tp) REVERT: F 82 ASN cc_start: 0.8471 (m-40) cc_final: 0.8122 (m-40) REVERT: F 89 VAL cc_start: 0.8516 (t) cc_final: 0.8239 (p) REVERT: I 140 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8153 (tp) REVERT: I 313 VAL cc_start: 0.8745 (m) cc_final: 0.8526 (t) REVERT: I 425 GLU cc_start: 0.8203 (tt0) cc_final: 0.7893 (tt0) REVERT: J 82 ASN cc_start: 0.8441 (m-40) cc_final: 0.8089 (m-40) REVERT: J 89 VAL cc_start: 0.8471 (t) cc_final: 0.8246 (p) outliers start: 58 outliers final: 44 residues processed: 443 average time/residue: 1.3618 time to fit residues: 682.5057 Evaluate side-chains 449 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 294 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain 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 309 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 443 ILE 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 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 380 VAL Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain E residue 439 THR 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 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 175 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101320 restraints weight = 24557.709| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.53 r_work: 0.3160 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19568 Z= 0.117 Angle : 0.604 12.994 26588 Z= 0.311 Chirality : 0.046 0.251 2904 Planarity : 0.004 0.052 3408 Dihedral : 5.351 36.639 2940 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.37 % Allowed : 15.58 % Favored : 82.05 % 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: -0.84 (0.17), residues: 2440 helix: -1.94 (0.78), residues: 24 sheet: 0.57 (0.17), residues: 912 loop : -1.33 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 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 0.006 0.000 ARG I 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 12) link_NAG-ASN : angle 2.48912 ( 36) hydrogen bonds : bond 0.03214 ( 540) hydrogen bonds : angle 5.16317 ( 1560) SS BOND : bond 0.00384 ( 36) SS BOND : angle 1.96294 ( 72) covalent geometry : bond 0.00273 (19520) covalent geometry : angle 0.58924 (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 468 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 418 time to evaluate : 2.248 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: 0.8281 (OUTLIER) cc_final: 0.7975 (mmm160) REVERT: A 234 ASN cc_start: 0.8082 (t0) cc_final: 0.7766 (t0) REVERT: A 391 GLN cc_start: 0.8460 (pt0) cc_final: 0.8151 (pt0) REVERT: A 431 LYS cc_start: 0.8043 (tppt) cc_final: 0.7807 (tppt) REVERT: A 432 GLU cc_start: 0.7882 (mp0) cc_final: 0.7538 (mp0) REVERT: H 89 VAL cc_start: 0.8492 (t) cc_final: 0.8221 (p) REVERT: B 234 ASN cc_start: 0.8207 (t0) cc_final: 0.7802 (t0) REVERT: B 247 THR cc_start: 0.8373 (p) cc_final: 0.8156 (t) REVERT: B 432 GLU cc_start: 0.7893 (mp0) cc_final: 0.7465 (mp0) REVERT: C 82 ASN cc_start: 0.8464 (m-40) cc_final: 0.8182 (m-40) REVERT: C 89 VAL cc_start: 0.8420 (t) cc_final: 0.8136 (p) REVERT: F 82 ASN cc_start: 0.8463 (m-40) cc_final: 0.8139 (m-40) REVERT: F 89 VAL cc_start: 0.8459 (t) cc_final: 0.8188 (p) REVERT: I 313 VAL cc_start: 0.8724 (m) cc_final: 0.8519 (t) REVERT: I 425 GLU cc_start: 0.8144 (tt0) cc_final: 0.7831 (tt0) REVERT: I 432 GLU cc_start: 0.7817 (mp0) cc_final: 0.7565 (mp0) REVERT: J 82 ASN cc_start: 0.8416 (m-40) cc_final: 0.8091 (m-40) REVERT: J 89 VAL cc_start: 0.8460 (t) cc_final: 0.8242 (p) outliers start: 50 outliers final: 37 residues processed: 444 average time/residue: 1.2512 time to fit residues: 627.3976 Evaluate side-chains 451 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 413 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 370 SER Chi-restraints excluded: chain A residue 380 VAL 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 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 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 380 VAL Chi-restraints excluded: chain E residue 439 THR 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 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain J residue 53 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.3782 > 50: distance: 7 - 10: 33.329 distance: 10 - 11: 39.933 distance: 11 - 14: 40.615 distance: 12 - 16: 24.321 distance: 16 - 17: 9.144 distance: 17 - 18: 41.866 distance: 18 - 19: 39.482 distance: 18 - 20: 39.003 distance: 20 - 21: 40.562 distance: 21 - 22: 39.087 distance: 21 - 24: 40.573 distance: 22 - 23: 25.067 distance: 22 - 26: 40.710 distance: 28 - 33: 11.903 distance: 33 - 34: 13.400 distance: 38 - 41: 39.009 distance: 39 - 46: 22.210 distance: 46 - 47: 44.072 distance: 47 - 48: 40.007 distance: 48 - 49: 55.359 distance: 48 - 52: 57.092 distance: 53 - 54: 53.646 distance: 53 - 56: 28.179 distance: 54 - 55: 41.574 distance: 54 - 59: 20.808 distance: 55 - 104: 28.954 distance: 56 - 57: 30.500 distance: 56 - 58: 10.023 distance: 59 - 60: 18.498 distance: 60 - 61: 46.120 distance: 61 - 62: 38.833 distance: 61 - 66: 16.762 distance: 63 - 65: 32.921 distance: 66 - 95: 36.624 distance: 67 - 68: 31.318 distance: 68 - 69: 38.894 distance: 68 - 74: 24.502 distance: 69 - 92: 31.778 distance: 70 - 72: 40.323