Starting phenix.real_space_refine on Wed Jan 22 19:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gav_29909/01_2025/8gav_29909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gav_29909/01_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_29909/01_2025/8gav_29909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gav_29909/01_2025/8gav_29909.map" model { file = "/net/cci-nas-00/data/ceres_data/8gav_29909/01_2025/8gav_29909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gav_29909/01_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-5571/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: 8.35, per 1000 atoms: 0.44 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=9, 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 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: 4.27 Conformation dependent library (CDL) restraints added in 2.7 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: 2.90 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: 7.70 Time building geometry restraints manager: 5.02 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: 10897 14.29 - 28.58: 575 28.58 - 42.87: 116 42.87 - 57.16: 35 57.16 - 71.45: 8 Dihedral angle restraints: 11631 sinusoidal: 4655 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 11628 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: 2.02 - 2.60: 139 2.60 - 3.17: 14319 3.17 - 3.75: 27019 3.75 - 4.32: 39680 4.32 - 4.90: 68660 Nonbonded interactions: 149817 Sorted by model distance: nonbonded pdb=" SG CYS I 175 " pdb=" SG CYS I 193 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS B 175 " pdb=" SG CYS B 193 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS E 175 " pdb=" SG CYS E 193 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS B 92 " pdb=" SG CYS B 417 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 92 " pdb=" SG CYS E 417 " model vdw 2.029 3.760 ... (remaining 149812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.900 Find NCS groups from input model: 0.360 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- 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 19520 Z= 0.704 Angle : 1.050 11.171 26480 Z= 0.583 Chirality : 0.069 0.219 2904 Planarity : 0.008 0.063 3408 Dihedral : 9.776 71.448 7180 Min Nonbonded Distance : 2.021 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 *********************** 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 : 2.063 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: 1.2148 time to fit residues: 682.1160 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 : 1.983 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9980 chunk 217 optimal weight: 2.9990 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 = 0.3486 r_free = 0.3486 target = 0.113931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099876 restraints weight = 24707.501| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.52 r_work: 0.3175 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19520 Z= 0.211 Angle : 0.620 6.061 26480 Z= 0.333 Chirality : 0.047 0.152 2904 Planarity : 0.005 0.055 3408 Dihedral : 7.005 55.412 2950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.23 % Allowed : 7.05 % Favored : 90.72 % 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: -2.20 (0.15), residues: 2440 helix: -2.98 (0.54), residues: 24 sheet: -0.67 (0.16), residues: 988 loop : -2.10 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 115 HIS 0.003 0.001 HIS A 310 PHE 0.018 0.002 PHE E 410 TYR 0.015 0.002 TYR L 32 ARG 0.007 0.001 ARG I 156 *********************** 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 494 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 447 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 234 ASN cc_start: 0.8076 (t0) cc_final: 0.7805 (t0) REVERT: A 425 GLU cc_start: 0.8177 (tt0) cc_final: 0.7878 (tt0) REVERT: A 431 LYS cc_start: 0.8223 (tppt) cc_final: 0.7995 (tppt) REVERT: A 432 GLU cc_start: 0.7779 (mp0) cc_final: 0.7449 (mp0) REVERT: H 89 VAL cc_start: 0.8545 (t) cc_final: 0.8211 (p) REVERT: B 92 CYS cc_start: 0.7651 (m) cc_final: 0.7337 (m) REVERT: B 234 ASN cc_start: 0.8178 (t0) cc_final: 0.7776 (t0) REVERT: B 417 CYS cc_start: 0.8243 (p) cc_final: 0.7967 (p) REVERT: B 432 GLU cc_start: 0.7763 (mp0) cc_final: 0.7355 (mp0) REVERT: C 89 VAL cc_start: 0.8562 (t) cc_final: 0.8226 (p) REVERT: E 92 CYS cc_start: 0.7607 (m) cc_final: 0.7340 (m) REVERT: E 385 ASN cc_start: 0.8216 (t0) cc_final: 0.7992 (t0) REVERT: E 417 CYS cc_start: 0.8181 (p) cc_final: 0.7940 (p) REVERT: E 425 GLU cc_start: 0.8256 (tt0) cc_final: 0.7953 (tt0) REVERT: F 89 VAL cc_start: 0.8524 (t) cc_final: 0.8237 (p) REVERT: I 271 SER cc_start: 0.8804 (p) cc_final: 0.8598 (m) REVERT: I 425 GLU cc_start: 0.8218 (tt0) cc_final: 0.7912 (tt0) REVERT: J 89 VAL cc_start: 0.8541 (t) cc_final: 0.8285 (p) outliers start: 47 outliers final: 20 residues processed: 465 average time/residue: 1.2121 time to fit residues: 640.8444 Evaluate side-chains 424 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 404 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 318 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 318 CYS 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: 0.5980 chunk 66 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.114876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100338 restraints weight = 24406.220| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.57 r_work: 0.3181 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19520 Z= 0.155 Angle : 0.549 6.152 26480 Z= 0.295 Chirality : 0.045 0.152 2904 Planarity : 0.004 0.049 3408 Dihedral : 5.779 35.866 2940 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.41 % Allowed : 10.46 % Favored : 87.12 % 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: -1.63 (0.16), residues: 2440 helix: -2.20 (0.73), residues: 24 sheet: -0.00 (0.17), residues: 916 loop : -1.86 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.002 PHE E 410 TYR 0.013 0.001 TYR H 91 ARG 0.004 0.000 ARG I 315 *********************** 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 475 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 424 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7963 (mmm160) REVERT: A 234 ASN cc_start: 0.8093 (t0) cc_final: 0.7793 (t0) REVERT: A 425 GLU cc_start: 0.8109 (tt0) cc_final: 0.7794 (tt0) REVERT: A 431 LYS cc_start: 0.8119 (tppt) cc_final: 0.7844 (tppt) REVERT: A 432 GLU cc_start: 0.7716 (mp0) cc_final: 0.7423 (mp0) REVERT: H 89 VAL cc_start: 0.8504 (t) cc_final: 0.8188 (p) REVERT: B 92 CYS cc_start: 0.7746 (m) cc_final: 0.7366 (m) REVERT: B 234 ASN cc_start: 0.8203 (t0) cc_final: 0.7771 (t0) REVERT: B 247 THR cc_start: 0.8312 (p) cc_final: 0.8083 (t) REVERT: B 277 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 432 GLU cc_start: 0.7738 (mp0) cc_final: 0.7339 (mp0) REVERT: B 435 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6564 (tm-30) REVERT: C 89 VAL cc_start: 0.8500 (t) cc_final: 0.8204 (p) REVERT: E 92 CYS cc_start: 0.7685 (m) cc_final: 0.7290 (m) REVERT: E 385 ASN cc_start: 0.8284 (t0) cc_final: 0.8057 (t0) REVERT: E 425 GLU cc_start: 0.8197 (tt0) cc_final: 0.7815 (tt0) REVERT: F 82 MET cc_start: 0.8171 (mtp) cc_final: 0.7963 (mtp) REVERT: F 89 VAL cc_start: 0.8512 (t) cc_final: 0.8252 (p) REVERT: I 425 GLU cc_start: 0.8168 (tt0) cc_final: 0.7826 (tt0) REVERT: I 431 LYS cc_start: 0.8109 (tppt) cc_final: 0.7851 (mppt) REVERT: J 82 MET cc_start: 0.8200 (mtp) cc_final: 0.7986 (mtp) REVERT: J 82 ASN cc_start: 0.8302 (m-40) cc_final: 0.7904 (m-40) REVERT: J 89 VAL cc_start: 0.8494 (t) cc_final: 0.8239 (p) outliers start: 51 outliers final: 27 residues processed: 447 average time/residue: 1.2887 time to fit residues: 652.5694 Evaluate side-chains 425 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 397 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 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 318 CYS Chi-restraints excluded: chain B residue 319 SER 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 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 318 CYS 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 318 CYS Chi-restraints excluded: chain I residue 325 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 175 optimal weight: 0.0170 chunk 192 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 0.0040 chunk 130 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.3430 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.115961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101430 restraints weight = 24548.180| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.58 r_work: 0.3200 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19520 Z= 0.133 Angle : 0.518 6.730 26480 Z= 0.277 Chirality : 0.044 0.145 2904 Planarity : 0.004 0.047 3408 Dihedral : 5.274 34.410 2940 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.60 % Allowed : 12.17 % Favored : 85.23 % 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: -1.28 (0.16), residues: 2440 helix: -1.80 (0.78), residues: 24 sheet: 0.11 (0.17), residues: 956 loop : -1.57 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 178 HIS 0.002 0.000 HIS A 310 PHE 0.013 0.002 PHE E 410 TYR 0.012 0.001 TYR H 91 ARG 0.004 0.000 ARG B 315 *********************** 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 468 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 413 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7899 (mmm160) REVERT: A 431 LYS cc_start: 0.8103 (tppt) cc_final: 0.7838 (tppt) REVERT: A 432 GLU cc_start: 0.7708 (mp0) cc_final: 0.7435 (mp0) REVERT: H 89 VAL cc_start: 0.8442 (t) cc_final: 0.8168 (p) REVERT: B 234 ASN cc_start: 0.8192 (t0) cc_final: 0.7775 (t0) REVERT: B 425 GLU cc_start: 0.8134 (tt0) cc_final: 0.7827 (tt0) REVERT: B 432 GLU cc_start: 0.7758 (mp0) cc_final: 0.7374 (mp0) REVERT: B 435 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6597 (tm-30) REVERT: C 82 ASN cc_start: 0.8472 (m-40) cc_final: 0.8189 (m-40) REVERT: E 385 ASN cc_start: 0.8345 (t0) cc_final: 0.8082 (t0) REVERT: E 400 ARG cc_start: 0.8252 (ptp-110) cc_final: 0.8047 (ptp-170) REVERT: E 425 GLU cc_start: 0.8148 (tt0) cc_final: 0.7782 (tt0) REVERT: F 82 ASN cc_start: 0.8365 (m-40) cc_final: 0.8021 (m-40) REVERT: F 89 VAL cc_start: 0.8441 (t) cc_final: 0.8187 (p) REVERT: J 82 ASN cc_start: 0.8360 (m-40) cc_final: 0.8027 (m-40) REVERT: J 89 VAL cc_start: 0.8416 (t) cc_final: 0.8185 (p) outliers start: 55 outliers final: 35 residues processed: 441 average time/residue: 1.3177 time to fit residues: 653.1865 Evaluate side-chains 436 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 400 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 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 317 VAL Chi-restraints excluded: chain B residue 318 CYS 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 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 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 317 VAL Chi-restraints excluded: chain I residue 318 CYS 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: 3.9990 chunk 215 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 226 GLN E 294 ASN G 37 GLN I 142 ASN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096935 restraints weight = 24754.492| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.56 r_work: 0.3128 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19520 Z= 0.405 Angle : 0.677 7.706 26480 Z= 0.357 Chirality : 0.049 0.148 2904 Planarity : 0.005 0.062 3408 Dihedral : 5.942 37.497 2940 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.94 % Allowed : 13.68 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2440 helix: -1.99 (0.77), residues: 24 sheet: 0.44 (0.17), residues: 900 loop : -1.63 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 178 HIS 0.008 0.002 HIS E 310 PHE 0.031 0.004 PHE B 205 TYR 0.024 0.003 TYR E 130 ARG 0.005 0.001 ARG A 420 *********************** 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 462 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 400 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (mmm160) REVERT: A 234 ASN cc_start: 0.8118 (t0) cc_final: 0.7857 (t0) REVERT: A 425 GLU cc_start: 0.8297 (tt0) cc_final: 0.7922 (tt0) REVERT: A 431 LYS cc_start: 0.8112 (tppt) cc_final: 0.7834 (tppt) REVERT: A 432 GLU cc_start: 0.7886 (mp0) cc_final: 0.7531 (mp0) REVERT: H 89 VAL cc_start: 0.8552 (t) cc_final: 0.8263 (p) REVERT: B 234 ASN cc_start: 0.8219 (t0) cc_final: 0.7819 (t0) REVERT: B 432 GLU cc_start: 0.7838 (mp0) cc_final: 0.7393 (mp0) REVERT: C 82 ASN cc_start: 0.8542 (m-40) cc_final: 0.8207 (m-40) REVERT: C 82 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 89 VAL cc_start: 0.8510 (t) cc_final: 0.8222 (p) REVERT: E 140 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8185 (tp) REVERT: F 82 ASN cc_start: 0.8484 (m-40) cc_final: 0.8137 (m-40) REVERT: F 89 VAL cc_start: 0.8550 (t) cc_final: 0.8293 (p) REVERT: I 140 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8167 (tp) REVERT: I 220 ASN cc_start: 0.8554 (m-40) cc_final: 0.8214 (m-40) REVERT: I 425 GLU cc_start: 0.8347 (tt0) cc_final: 0.8011 (tt0) REVERT: J 82 ASN cc_start: 0.8487 (m-40) cc_final: 0.8129 (m-40) REVERT: J 82 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8361 (mp) REVERT: J 89 VAL cc_start: 0.8525 (t) cc_final: 0.8296 (p) outliers start: 62 outliers final: 47 residues processed: 430 average time/residue: 1.2867 time to fit residues: 624.8192 Evaluate side-chains 447 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 395 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain 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 337 CYS 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 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 91 ILE Chi-restraints excluded: chain I residue 101 SER 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 317 VAL Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 82 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 204 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 237 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101364 restraints weight = 24900.848| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.57 r_work: 0.3153 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19520 Z= 0.185 Angle : 0.567 7.182 26480 Z= 0.301 Chirality : 0.045 0.151 2904 Planarity : 0.004 0.047 3408 Dihedral : 5.479 36.826 2940 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.89 % Allowed : 14.39 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2440 helix: -1.96 (0.78), residues: 24 sheet: 0.36 (0.17), residues: 920 loop : -1.51 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.002 PHE A 410 TYR 0.015 0.001 TYR H 91 ARG 0.004 0.000 ARG A 315 *********************** 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 464 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8033 (mmm160) REVERT: A 234 ASN cc_start: 0.8055 (t0) cc_final: 0.7744 (t0) REVERT: A 431 LYS cc_start: 0.8072 (tppt) cc_final: 0.7819 (tppt) REVERT: A 432 GLU cc_start: 0.7879 (mp0) cc_final: 0.7548 (mp0) REVERT: H 82 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8412 (mp) REVERT: H 89 VAL cc_start: 0.8517 (t) cc_final: 0.8242 (p) REVERT: L 22 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8241 (t) REVERT: B 234 ASN cc_start: 0.8163 (t0) cc_final: 0.7746 (t0) REVERT: B 432 GLU cc_start: 0.7929 (mp0) cc_final: 0.7489 (mp0) REVERT: C 82 ASN cc_start: 0.8470 (m-40) cc_final: 0.8186 (m-40) REVERT: C 89 VAL cc_start: 0.8451 (t) cc_final: 0.8152 (p) REVERT: F 82 ASN cc_start: 0.8435 (m-40) cc_final: 0.8106 (m-40) REVERT: F 89 VAL cc_start: 0.8483 (t) cc_final: 0.8213 (p) REVERT: G 46 LEU cc_start: 0.8635 (tp) cc_final: 0.8426 (tt) REVERT: I 140 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8160 (tp) REVERT: J 82 ASN cc_start: 0.8412 (m-40) cc_final: 0.8075 (m-40) REVERT: J 89 VAL cc_start: 0.8461 (t) cc_final: 0.8247 (p) outliers start: 61 outliers final: 43 residues processed: 436 average time/residue: 1.3197 time to fit residues: 647.6629 Evaluate side-chains 445 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS 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 D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 337 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 443 ILE 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 101 SER 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 318 CYS Chi-restraints excluded: chain I residue 325 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 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: 0.3980 chunk 133 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100840 restraints weight = 24694.414| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.56 r_work: 0.3144 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19520 Z= 0.229 Angle : 0.589 8.041 26480 Z= 0.311 Chirality : 0.046 0.156 2904 Planarity : 0.004 0.045 3408 Dihedral : 5.496 36.704 2940 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.94 % Allowed : 15.25 % Favored : 81.82 % 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: -0.92 (0.16), residues: 2440 helix: -1.92 (0.78), residues: 24 sheet: 0.59 (0.18), residues: 896 loop : -1.42 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 178 HIS 0.004 0.001 HIS A 336 PHE 0.018 0.002 PHE B 205 TYR 0.016 0.001 TYR H 91 ARG 0.011 0.000 ARG E 292 *********************** 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: 62 poor density : 398 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8042 (mmm160) REVERT: A 234 ASN cc_start: 0.8063 (t0) cc_final: 0.7750 (t0) REVERT: A 431 LYS cc_start: 0.8064 (tppt) cc_final: 0.7808 (tppt) REVERT: A 432 GLU cc_start: 0.7892 (mp0) cc_final: 0.7545 (mp0) REVERT: H 89 VAL cc_start: 0.8487 (t) cc_final: 0.8216 (p) REVERT: L 22 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8230 (t) REVERT: B 234 ASN cc_start: 0.8184 (t0) cc_final: 0.7750 (t0) REVERT: B 277 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 432 GLU cc_start: 0.7940 (mp0) cc_final: 0.7475 (mp0) REVERT: C 82 ASN cc_start: 0.8493 (m-40) cc_final: 0.8212 (m-40) REVERT: C 89 VAL cc_start: 0.8432 (t) cc_final: 0.8149 (p) REVERT: D 46 LEU cc_start: 0.8556 (tp) cc_final: 0.8332 (tt) REVERT: E 140 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8155 (tp) REVERT: F 82 ASN cc_start: 0.8463 (m-40) cc_final: 0.8113 (m-40) REVERT: F 89 VAL cc_start: 0.8483 (t) cc_final: 0.8216 (p) REVERT: G 46 LEU cc_start: 0.8625 (tp) cc_final: 0.8425 (tt) REVERT: I 140 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8136 (tp) REVERT: I 431 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7706 (mppt) REVERT: I 432 GLU cc_start: 0.7946 (mp0) cc_final: 0.7637 (mp0) REVERT: J 82 ASN cc_start: 0.8456 (m-40) cc_final: 0.8108 (m-40) REVERT: J 89 VAL cc_start: 0.8440 (t) cc_final: 0.8230 (p) outliers start: 62 outliers final: 46 residues processed: 434 average time/residue: 1.3257 time to fit residues: 657.2200 Evaluate side-chains 445 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 394 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 380 VAL 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 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 370 SER 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 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 443 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 101 SER 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 317 VAL Chi-restraints excluded: chain I residue 318 CYS 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 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: 0.9980 chunk 217 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 185 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 294 ASN D 37 GLN E 226 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 = 0.3487 r_free = 0.3487 target = 0.116293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101686 restraints weight = 24783.491| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.57 r_work: 0.3158 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19520 Z= 0.174 Angle : 0.562 8.555 26480 Z= 0.296 Chirality : 0.045 0.153 2904 Planarity : 0.004 0.040 3408 Dihedral : 5.322 36.636 2940 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.70 % Allowed : 15.29 % Favored : 82.01 % 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: -1.87 (0.78), residues: 24 sheet: 0.52 (0.18), residues: 916 loop : -1.30 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 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 0.010 0.000 ARG E 292 *********************** 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: 57 poor density : 408 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7977 (mmm160) REVERT: A 234 ASN cc_start: 0.8046 (t0) cc_final: 0.7733 (t0) REVERT: A 431 LYS cc_start: 0.8053 (tppt) cc_final: 0.7811 (tppt) REVERT: A 432 GLU cc_start: 0.7869 (mp0) cc_final: 0.7544 (mp0) REVERT: H 89 VAL cc_start: 0.8478 (t) cc_final: 0.8217 (p) REVERT: B 425 GLU cc_start: 0.8187 (tt0) cc_final: 0.7890 (tt0) REVERT: B 432 GLU cc_start: 0.7909 (mp0) cc_final: 0.7476 (mp0) REVERT: C 82 ASN cc_start: 0.8470 (m-40) cc_final: 0.8198 (m-40) REVERT: C 89 VAL cc_start: 0.8401 (t) cc_final: 0.8120 (p) REVERT: D 46 LEU cc_start: 0.8555 (tp) cc_final: 0.8330 (tt) REVERT: E 425 GLU cc_start: 0.8169 (tt0) cc_final: 0.7908 (tt0) REVERT: F 82 ASN cc_start: 0.8440 (m-40) cc_final: 0.8109 (m-40) REVERT: F 89 VAL cc_start: 0.8440 (t) cc_final: 0.8172 (p) REVERT: I 431 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7561 (mppt) REVERT: I 432 GLU cc_start: 0.7904 (mp0) cc_final: 0.7627 (mp0) REVERT: J 82 ASN cc_start: 0.8418 (m-40) cc_final: 0.8092 (m-40) REVERT: J 89 VAL cc_start: 0.8424 (t) cc_final: 0.8210 (p) outliers start: 57 outliers final: 45 residues processed: 438 average time/residue: 1.3350 time to fit residues: 657.7642 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 397 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 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 B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 319 SER 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 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 399 ASP Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN L 37 GLN B 294 ASN D 37 GLN E 245 ASN E 294 ASN G 37 GLN I 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 = 0.3489 r_free = 0.3489 target = 0.116517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101872 restraints weight = 24714.325| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.56 r_work: 0.3158 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19520 Z= 0.179 Angle : 0.570 8.702 26480 Z= 0.298 Chirality : 0.045 0.219 2904 Planarity : 0.004 0.038 3408 Dihedral : 5.317 36.657 2940 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.60 % Allowed : 15.62 % Favored : 81.77 % 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: -0.78 (0.17), residues: 2440 helix: -1.79 (0.80), residues: 24 sheet: 0.62 (0.18), residues: 908 loop : -1.29 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.006 0.001 HIS A 336 PHE 0.016 0.002 PHE A 410 TYR 0.017 0.001 TYR H 91 ARG 0.009 0.000 ARG E 292 *********************** 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 457 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 402 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7985 (mmm160) REVERT: A 234 ASN cc_start: 0.8049 (t0) cc_final: 0.7736 (t0) REVERT: A 391 GLN cc_start: 0.8472 (pt0) cc_final: 0.8151 (pt0) REVERT: A 431 LYS cc_start: 0.8048 (tppt) cc_final: 0.7808 (tppt) REVERT: A 432 GLU cc_start: 0.7880 (mp0) cc_final: 0.7552 (mp0) REVERT: H 89 VAL cc_start: 0.8473 (t) cc_final: 0.8220 (p) REVERT: B 234 ASN cc_start: 0.8177 (t0) cc_final: 0.7729 (t0) REVERT: B 277 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 432 GLU cc_start: 0.7894 (mp0) cc_final: 0.7462 (mp0) REVERT: C 82 ASN cc_start: 0.8456 (m-40) cc_final: 0.8180 (m-40) REVERT: C 89 VAL cc_start: 0.8389 (t) cc_final: 0.8113 (p) REVERT: D 46 LEU cc_start: 0.8544 (tp) cc_final: 0.8316 (tt) REVERT: E 140 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8130 (tp) REVERT: F 82 ASN cc_start: 0.8448 (m-40) cc_final: 0.8127 (m-40) REVERT: F 89 VAL cc_start: 0.8444 (t) cc_final: 0.8179 (p) REVERT: I 140 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8124 (tp) REVERT: I 431 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7535 (mppt) REVERT: I 432 GLU cc_start: 0.7873 (mp0) cc_final: 0.7598 (mp0) REVERT: J 82 ASN cc_start: 0.8429 (m-40) cc_final: 0.8097 (m-40) REVERT: J 89 VAL cc_start: 0.8423 (t) cc_final: 0.8215 (p) outliers start: 55 outliers final: 49 residues processed: 432 average time/residue: 1.3816 time to fit residues: 671.4095 Evaluate side-chains 451 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 398 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 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 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 317 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 319 SER 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 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 249 LYS 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 G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 101 SER 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 317 VAL Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain I residue 431 LYS 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 ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 157 optimal weight: 0.0060 chunk 231 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 194 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN L 37 GLN B 294 ASN D 37 GLN E 294 ASN G 37 GLN I 245 ASN 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 = 0.3494 r_free = 0.3494 target = 0.116943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102350 restraints weight = 24682.472| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.56 r_work: 0.3163 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19520 Z= 0.169 Angle : 0.560 8.103 26480 Z= 0.293 Chirality : 0.045 0.178 2904 Planarity : 0.004 0.037 3408 Dihedral : 5.237 36.642 2940 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % Favored : 81.96 % 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: -0.77 (0.17), residues: 2440 helix: -1.72 (0.80), residues: 24 sheet: 0.56 (0.18), residues: 920 loop : -1.25 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.002 PHE A 410 TYR 0.017 0.001 TYR H 91 ARG 0.009 0.000 ARG E 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 404 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (mmm160) REVERT: A 234 ASN cc_start: 0.8047 (t0) cc_final: 0.7721 (t0) REVERT: A 306 ASN cc_start: 0.8522 (t0) cc_final: 0.8231 (t0) REVERT: A 391 GLN cc_start: 0.8436 (pt0) cc_final: 0.8126 (pt0) REVERT: A 431 LYS cc_start: 0.8036 (tppt) cc_final: 0.7778 (tppt) REVERT: A 432 GLU cc_start: 0.7874 (mp0) cc_final: 0.7540 (mp0) REVERT: H 89 VAL cc_start: 0.8468 (t) cc_final: 0.8224 (p) REVERT: B 432 GLU cc_start: 0.7895 (mp0) cc_final: 0.7458 (mp0) REVERT: C 82 ASN cc_start: 0.8459 (m-40) cc_final: 0.8192 (m-40) REVERT: E 140 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8141 (tp) REVERT: F 82 ASN cc_start: 0.8437 (m-40) cc_final: 0.8115 (m-40) REVERT: F 89 VAL cc_start: 0.8429 (t) cc_final: 0.8169 (p) REVERT: I 140 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8132 (tp) REVERT: I 431 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7493 (mppt) REVERT: I 432 GLU cc_start: 0.7842 (mp0) cc_final: 0.7575 (mp0) REVERT: J 82 ASN cc_start: 0.8389 (m-40) cc_final: 0.8073 (m-40) REVERT: J 89 VAL cc_start: 0.8409 (t) cc_final: 0.8201 (p) outliers start: 58 outliers final: 47 residues processed: 436 average time/residue: 1.3451 time to fit residues: 663.4066 Evaluate side-chains 446 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS 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 D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 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 249 LYS Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 101 SER 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 317 VAL Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 431 LYS 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-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 63.6608 > 50: distance: 33 - 146: 3.216 distance: 55 - 65: 15.799 distance: 65 - 66: 17.773 distance: 65 - 71: 24.689 distance: 66 - 67: 33.853 distance: 66 - 69: 25.656 distance: 67 - 68: 6.647 distance: 67 - 72: 52.074 distance: 69 - 70: 14.775 distance: 70 - 71: 15.461 distance: 72 - 73: 14.420 distance: 73 - 74: 13.442 distance: 73 - 76: 15.118 distance: 74 - 75: 18.394 distance: 74 - 83: 25.485 distance: 76 - 77: 16.179 distance: 77 - 78: 31.766 distance: 78 - 79: 6.871 distance: 79 - 80: 15.561 distance: 80 - 81: 4.746 distance: 80 - 82: 14.282 distance: 83 - 84: 9.895 distance: 84 - 85: 3.710 distance: 84 - 87: 7.545 distance: 85 - 86: 3.731 distance: 85 - 95: 4.814 distance: 87 - 88: 10.506 distance: 88 - 89: 9.235 distance: 88 - 90: 5.299 distance: 89 - 91: 10.463 distance: 90 - 92: 6.542 distance: 91 - 93: 4.901 distance: 92 - 93: 4.734 distance: 93 - 94: 4.763 distance: 95 - 96: 29.575 distance: 95 - 101: 7.542 distance: 96 - 97: 12.711 distance: 96 - 99: 34.862 distance: 97 - 98: 63.661 distance: 97 - 102: 13.402 distance: 99 - 100: 22.694 distance: 100 - 101: 21.918 distance: 102 - 103: 9.404 distance: 103 - 104: 26.678 distance: 104 - 105: 18.367 distance: 104 - 106: 18.203 distance: 106 - 107: 22.785 distance: 106 - 191: 15.722 distance: 107 - 108: 11.343 distance: 107 - 110: 18.279 distance: 108 - 109: 33.050 distance: 108 - 113: 9.360 distance: 109 - 188: 27.974 distance: 110 - 111: 32.964 distance: 110 - 112: 11.871 distance: 113 - 114: 3.777 distance: 114 - 115: 17.322 distance: 114 - 117: 5.639 distance: 115 - 116: 10.550 distance: 115 - 124: 21.446 distance: 117 - 118: 8.292 distance: 118 - 119: 5.338 distance: 119 - 120: 5.365 distance: 120 - 121: 4.842 distance: 121 - 122: 6.697 distance: 121 - 123: 6.505 distance: 124 - 125: 5.410 distance: 124 - 175: 7.947 distance: 125 - 126: 12.804 distance: 125 - 128: 5.020 distance: 126 - 127: 7.892 distance: 126 - 130: 15.396 distance: 127 - 172: 19.019 distance: 128 - 129: 18.691 distance: 130 - 131: 4.678 distance: 131 - 132: 8.287 distance: 132 - 133: 13.452 distance: 132 - 137: 10.604 distance: 134 - 135: 5.871 distance: 134 - 136: 6.781 distance: 137 - 138: 13.416 distance: 137 - 161: 15.233 distance: 138 - 139: 21.626 distance: 138 - 141: 10.896 distance: 139 - 140: 21.410 distance: 139 - 143: 19.895 distance: 141 - 142: 16.060