Starting phenix.real_space_refine on Tue Nov 19 08:39:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_29909.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_29909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_29909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_29909.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gav_29909/11_2024/8gav_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-5513/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: 8.77, per 1000 atoms: 0.46 Number of scatterers: 19088 At special positions: 0 Unit cell: (132.09, 132.09, 96.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3788 8.00 N 3320 7.00 C 11860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=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: 4.64 Conformation dependent library (CDL) restraints added in 2.5 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 56 sheets defined 3.6% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER B 145 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA E 110 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER E 145 " --> pdb=" O ASN E 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN E 146 " --> pdb=" O VAL E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 146' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER F 87 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 removed outlier: 3.893A pdb=" N ALA I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.515A pdb=" N SER I 145 " --> pdb=" O ASN I 142 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN I 146 " --> pdb=" O VAL I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASP J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 83 through 87 removed outlier: 4.066A pdb=" N SER J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 408 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 236 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR A 252 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU A 372 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 400 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR A 376 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL A 396 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG A 394 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=10, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 93 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 93 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL L 19 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR L 95A" --> pdb=" O GLU L 92 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 408 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA B 133 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 236 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR B 252 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 254 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 261 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 311 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU B 372 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG B 400 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 376 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 396 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS B 378 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG B 394 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 428 through 429 Processing sheet with id=22, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=24, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 93 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 93 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL D 19 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 95A" --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY E 96 " --> pdb=" O THR E 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL E 445 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS E 102 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE E 443 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG E 420 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 408 " --> pdb=" O TYR E 423 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA E 133 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 157 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS E 175 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET E 160 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN E 173 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER E 179 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP E 213 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR E 207 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU E 211 " --> pdb=" O TYR E 207 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'E' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 236 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR E 252 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS E 267 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE E 254 " --> pdb=" O THR E 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR E 265 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE E 256 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS E 261 " --> pdb=" O GLU E 258 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'E' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS E 278 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 290 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS E 280 " --> pdb=" O ARG E 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG E 288 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY E 286 " --> pdb=" O PRO E 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 311 " --> pdb=" O ASN E 306 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU E 372 " --> pdb=" O ARG E 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG E 400 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR E 376 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL E 396 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS E 378 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG E 394 " --> pdb=" O LYS E 378 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 428 through 429 Processing sheet with id=36, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 78 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=38, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA F 93 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL G 19 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR G 95A" --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 96 through 102 removed outlier: 3.785A pdb=" N GLY I 96 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL I 445 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS I 102 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE I 443 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY I 408 " --> pdb=" O TYR I 423 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 121 through 124 removed outlier: 3.656A pdb=" N ALA I 133 " --> pdb=" O LEU I 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS I 175 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET I 160 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN I 173 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'I' and resid 179 through 184 removed outlier: 3.526A pdb=" N SER I 179 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP I 213 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'I' and resid 231 through 233 removed outlier: 4.028A pdb=" N VAL I 231 " --> pdb=" O THR I 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 236 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR I 252 " --> pdb=" O LYS I 267 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS I 267 " --> pdb=" O THR I 252 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE I 254 " --> pdb=" O THR I 265 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR I 265 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE I 256 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS I 261 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'I' and resid 276 through 283 removed outlier: 4.892A pdb=" N CYS I 278 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL I 290 " --> pdb=" O CYS I 278 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS I 280 " --> pdb=" O ARG I 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG I 288 " --> pdb=" O CYS I 280 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY I 286 " --> pdb=" O PRO I 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 311 " --> pdb=" O ASN I 306 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'I' and resid 353 through 356 removed outlier: 6.305A pdb=" N LEU I 372 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG I 400 " --> pdb=" O LEU I 372 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR I 376 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL I 396 " --> pdb=" O THR I 376 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LYS I 378 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG I 394 " --> pdb=" O LYS I 378 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'I' and resid 428 through 429 Processing sheet with id=50, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.523A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL J 78 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=52, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 93 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 93 " --> pdb=" O THR J 35 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.539A pdb=" N VAL K 19 " --> pdb=" O VAL K 75 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.579A pdb=" N ALA K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR K 95A" --> pdb=" O GLU K 92 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.74 Time building geometry restraints manager: 5.47 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: 0.00 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: 1.690 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.920 Find NCS groups from input model: 0.610 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- 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 : 2.286 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: 1.2263 time to fit residues: 687.4216 Evaluate side-chains 420 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 411 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 1.929 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6445 (m) cc_final: 0.6236 (m) REVERT: A 234 ASN cc_start: 0.7464 (t0) cc_final: 0.7250 (t0) REVERT: A 271 SER cc_start: 0.8719 (p) cc_final: 0.8516 (m) REVERT: A 425 GLU cc_start: 0.7848 (tt0) cc_final: 0.7558 (tt0) REVERT: A 432 GLU cc_start: 0.7177 (mp0) cc_final: 0.6917 (mp0) REVERT: H 89 VAL cc_start: 0.8457 (t) cc_final: 0.8110 (p) REVERT: B 92 CYS cc_start: 0.6806 (m) cc_final: 0.6491 (m) REVERT: B 234 ASN cc_start: 0.7542 (t0) cc_final: 0.7242 (t0) REVERT: B 432 GLU cc_start: 0.7133 (mp0) cc_final: 0.6818 (mp0) REVERT: C 89 VAL cc_start: 0.8463 (t) cc_final: 0.8113 (p) REVERT: E 92 CYS cc_start: 0.6767 (m) cc_final: 0.6514 (m) REVERT: E 239 VAL cc_start: 0.8819 (p) cc_final: 0.8606 (t) REVERT: E 425 GLU cc_start: 0.7900 (tt0) cc_final: 0.7616 (tt0) REVERT: F 89 VAL cc_start: 0.8414 (t) cc_final: 0.8094 (p) REVERT: I 271 SER cc_start: 0.8689 (p) cc_final: 0.8485 (m) REVERT: I 425 GLU cc_start: 0.7936 (tt0) cc_final: 0.7637 (tt0) REVERT: J 89 VAL cc_start: 0.8418 (t) cc_final: 0.8107 (p) outliers start: 47 outliers final: 20 residues processed: 465 average time/residue: 1.2266 time to fit residues: 648.8887 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 : 2.191 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 E 385 ASN G 37 GLN I 226 GLN I 294 ASN I 358 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1955 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= 0.205 Angle : 0.581 6.203 26480 Z= 0.312 Chirality : 0.046 0.152 2904 Planarity : 0.005 0.050 3408 Dihedral : 5.974 36.890 2940 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.51 % Allowed : 10.27 % Favored : 87.22 % 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: 0.02 (0.17), residues: 916 loop : -1.88 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 178 HIS 0.004 0.001 HIS A 336 PHE 0.018 0.002 PHE B 205 TYR 0.014 0.002 TYR H 91 ARG 0.003 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: 53 poor density : 422 time to evaluate : 2.224 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6436 (m) cc_final: 0.6219 (m) REVERT: A 118 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7938 (mmm160) REVERT: A 234 ASN cc_start: 0.7480 (t0) cc_final: 0.7252 (t0) REVERT: A 425 GLU cc_start: 0.7819 (tt0) cc_final: 0.7517 (tt0) REVERT: A 432 GLU cc_start: 0.7162 (mp0) cc_final: 0.6918 (mp0) REVERT: H 89 VAL cc_start: 0.8435 (t) cc_final: 0.8109 (p) REVERT: B 234 ASN cc_start: 0.7549 (t0) cc_final: 0.7238 (t0) REVERT: B 432 GLU cc_start: 0.7127 (mp0) cc_final: 0.6829 (mp0) REVERT: B 435 GLU cc_start: 0.6161 (tm-30) cc_final: 0.5815 (tm-30) REVERT: C 82 MET cc_start: 0.7883 (mtp) cc_final: 0.7667 (mtp) REVERT: C 89 VAL cc_start: 0.8388 (t) cc_final: 0.8091 (p) REVERT: F 89 VAL cc_start: 0.8380 (t) cc_final: 0.8096 (p) REVERT: I 425 GLU cc_start: 0.7918 (tt0) cc_final: 0.7597 (tt0) REVERT: J 82 MET cc_start: 0.7871 (mtp) cc_final: 0.7590 (mtp) REVERT: J 82 ASN cc_start: 0.8247 (m-40) cc_final: 0.7840 (m-40) REVERT: J 89 VAL cc_start: 0.8355 (t) cc_final: 0.8059 (p) outliers start: 53 outliers final: 30 residues processed: 446 average time/residue: 1.3369 time to fit residues: 671.1887 Evaluate side-chains 427 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 396 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 309 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 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 309 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 0.4980 chunk 114 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 385 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19520 Z= 0.257 Angle : 0.603 5.994 26480 Z= 0.322 Chirality : 0.047 0.147 2904 Planarity : 0.005 0.050 3408 Dihedral : 5.856 37.333 2940 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.75 % Allowed : 12.59 % Favored : 84.66 % 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: -1.35 (0.16), residues: 2440 helix: -2.04 (0.76), residues: 24 sheet: 0.25 (0.17), residues: 908 loop : -1.70 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 178 HIS 0.006 0.001 HIS A 336 PHE 0.022 0.003 PHE B 205 TYR 0.017 0.002 TYR E 130 ARG 0.003 0.000 ARG I 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 462 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 404 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6447 (m) cc_final: 0.6233 (m) REVERT: A 118 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7983 (mmm160) REVERT: A 234 ASN cc_start: 0.7475 (t0) cc_final: 0.7236 (t0) REVERT: A 425 GLU cc_start: 0.7814 (tt0) cc_final: 0.7530 (tt0) REVERT: A 432 GLU cc_start: 0.7174 (mp0) cc_final: 0.6936 (mp0) REVERT: H 89 VAL cc_start: 0.8416 (t) cc_final: 0.8103 (p) REVERT: H 94 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7808 (ptt-90) REVERT: B 234 ASN cc_start: 0.7549 (t0) cc_final: 0.7231 (t0) REVERT: B 432 GLU cc_start: 0.7165 (mp0) cc_final: 0.6848 (mp0) REVERT: C 82 ASN cc_start: 0.8352 (m-40) cc_final: 0.8055 (m-40) REVERT: C 89 VAL cc_start: 0.8394 (t) cc_final: 0.8085 (p) REVERT: C 94 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7702 (ptt-90) REVERT: F 82 ASN cc_start: 0.8367 (m-40) cc_final: 0.7997 (m-40) REVERT: F 89 VAL cc_start: 0.8375 (t) cc_final: 0.8091 (p) REVERT: I 313 VAL cc_start: 0.8601 (m) cc_final: 0.8376 (t) REVERT: I 425 GLU cc_start: 0.7926 (tt0) cc_final: 0.7635 (tt0) REVERT: J 82 MET cc_start: 0.7821 (mtp) cc_final: 0.7466 (mtp) REVERT: J 82 ASN cc_start: 0.8312 (m-40) cc_final: 0.7959 (m-40) REVERT: J 89 VAL cc_start: 0.8346 (t) cc_final: 0.8065 (p) REVERT: J 94 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7722 (ptt-90) outliers start: 58 outliers final: 36 residues processed: 431 average time/residue: 1.3840 time to fit residues: 671.3531 Evaluate side-chains 429 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 389 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 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 H residue 94 ARG 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 318 CYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 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 443 ILE Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 245 ASN B 294 ASN D 37 GLN E 226 GLN E 294 ASN E 385 ASN G 37 GLN I 226 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19520 Z= 0.335 Angle : 0.645 6.758 26480 Z= 0.343 Chirality : 0.048 0.198 2904 Planarity : 0.005 0.052 3408 Dihedral : 5.947 37.763 2940 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.08 % Allowed : 13.35 % Favored : 83.57 % 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: -1.24 (0.16), residues: 2440 helix: -2.06 (0.75), residues: 24 sheet: 0.42 (0.17), residues: 900 loop : -1.69 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 178 HIS 0.008 0.001 HIS A 336 PHE 0.027 0.003 PHE B 205 TYR 0.019 0.002 TYR E 130 ARG 0.004 0.001 ARG I 288 *********************** 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 464 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 399 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6413 (m) cc_final: 0.6179 (m) REVERT: A 118 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8023 (mmm160) REVERT: A 234 ASN cc_start: 0.7483 (t0) cc_final: 0.7246 (t0) REVERT: A 425 GLU cc_start: 0.7861 (tt0) cc_final: 0.7532 (tt0) REVERT: A 432 GLU cc_start: 0.7216 (mp0) cc_final: 0.6935 (mp0) REVERT: H 89 VAL cc_start: 0.8442 (t) cc_final: 0.8121 (p) REVERT: H 94 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7789 (ptt-90) REVERT: L 22 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8135 (t) REVERT: B 234 ASN cc_start: 0.7555 (t0) cc_final: 0.7242 (t0) REVERT: B 432 GLU cc_start: 0.7196 (mp0) cc_final: 0.6860 (mp0) REVERT: C 82 ASN cc_start: 0.8414 (m-40) cc_final: 0.8096 (m-40) REVERT: C 89 VAL cc_start: 0.8389 (t) cc_final: 0.8101 (p) REVERT: C 94 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7670 (ptt-90) REVERT: F 82 ASN cc_start: 0.8429 (m-40) cc_final: 0.8056 (m-40) REVERT: F 89 VAL cc_start: 0.8402 (t) cc_final: 0.8110 (p) REVERT: G 46 LEU cc_start: 0.8472 (tp) cc_final: 0.8253 (tt) REVERT: I 172 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: I 313 VAL cc_start: 0.8623 (m) cc_final: 0.8405 (t) REVERT: I 425 GLU cc_start: 0.7938 (tt0) cc_final: 0.7628 (tt0) REVERT: J 82 ASN cc_start: 0.8347 (m-40) cc_final: 0.7982 (m-40) REVERT: J 82 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8299 (mp) REVERT: J 89 VAL cc_start: 0.8378 (t) cc_final: 0.8083 (p) REVERT: J 94 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7773 (ptt-90) outliers start: 65 outliers final: 42 residues processed: 430 average time/residue: 1.3278 time to fit residues: 642.7587 Evaluate side-chains 442 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 393 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 172 LYS 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 J residue 62 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN E 385 ASN G 37 GLN ** I 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 19520 Z= 0.572 Angle : 0.778 7.991 26480 Z= 0.411 Chirality : 0.054 0.212 2904 Planarity : 0.006 0.088 3408 Dihedral : 6.420 39.646 2940 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 3.55 % Allowed : 13.97 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.37 (0.16), residues: 2440 helix: -2.27 (0.66), residues: 24 sheet: 0.25 (0.17), residues: 944 loop : -1.78 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 178 HIS 0.011 0.002 HIS A 336 PHE 0.034 0.004 PHE A 205 TYR 0.023 0.003 TYR F 91 ARG 0.007 0.001 ARG J 94 *********************** 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 472 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 397 time to evaluate : 2.283 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6343 (m) cc_final: 0.6093 (m) REVERT: A 118 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8147 (mmm160) REVERT: A 234 ASN cc_start: 0.7554 (t0) cc_final: 0.7348 (t0) REVERT: A 425 GLU cc_start: 0.7960 (tt0) cc_final: 0.7610 (tt0) REVERT: A 432 GLU cc_start: 0.7268 (mp0) cc_final: 0.6979 (mp0) REVERT: H 89 VAL cc_start: 0.8517 (t) cc_final: 0.8187 (p) REVERT: H 94 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7832 (ptt-90) REVERT: B 234 ASN cc_start: 0.7620 (t0) cc_final: 0.7296 (t0) REVERT: C 82 ASN cc_start: 0.8446 (m-40) cc_final: 0.8094 (m-40) REVERT: C 89 VAL cc_start: 0.8465 (t) cc_final: 0.8115 (p) REVERT: C 94 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7739 (ptt-90) REVERT: F 82 ASN cc_start: 0.8446 (m-40) cc_final: 0.8053 (m-40) REVERT: F 89 VAL cc_start: 0.8468 (t) cc_final: 0.8139 (p) REVERT: I 140 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8100 (tp) REVERT: I 172 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7857 (mtmt) REVERT: I 313 VAL cc_start: 0.8654 (m) cc_final: 0.8424 (t) REVERT: I 425 GLU cc_start: 0.8035 (tt0) cc_final: 0.7744 (tt0) REVERT: J 82 ASN cc_start: 0.8433 (m-40) cc_final: 0.8068 (m-40) REVERT: J 89 VAL cc_start: 0.8439 (t) cc_final: 0.8131 (p) REVERT: J 94 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7763 (ptt-90) outliers start: 75 outliers final: 51 residues processed: 435 average time/residue: 1.3065 time to fit residues: 641.4818 Evaluate side-chains 451 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 394 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 370 SER 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 H residue 94 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain 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 172 LYS Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 271 SER Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 307 ILE 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 J residue 62 SER Chi-restraints excluded: chain J residue 94 ARG Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 0.0770 chunk 144 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 385 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19520 Z= 0.187 Angle : 0.584 9.963 26480 Z= 0.311 Chirality : 0.046 0.148 2904 Planarity : 0.004 0.049 3408 Dihedral : 5.632 37.795 2940 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.75 % Allowed : 14.77 % Favored : 82.48 % 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: -1.10 (0.16), residues: 2440 helix: -2.07 (0.74), residues: 24 sheet: 0.37 (0.17), residues: 920 loop : -1.50 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 178 HIS 0.004 0.001 HIS A 336 PHE 0.016 0.002 PHE A 410 TYR 0.016 0.001 TYR E 281 ARG 0.007 0.000 ARG I 288 *********************** 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 465 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 407 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6401 (m) cc_final: 0.6151 (m) REVERT: A 118 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7912 (mmm160) REVERT: A 234 ASN cc_start: 0.7467 (t0) cc_final: 0.7203 (t0) REVERT: A 432 GLU cc_start: 0.7176 (mp0) cc_final: 0.6920 (mp0) REVERT: H 82 ASN cc_start: 0.8370 (m-40) cc_final: 0.7973 (m-40) REVERT: H 89 VAL cc_start: 0.8439 (t) cc_final: 0.8136 (p) REVERT: B 234 ASN cc_start: 0.7514 (t0) cc_final: 0.7194 (t0) REVERT: B 432 GLU cc_start: 0.7214 (mp0) cc_final: 0.6871 (mp0) REVERT: C 82 ASN cc_start: 0.8390 (m-40) cc_final: 0.8107 (m-40) REVERT: C 89 VAL cc_start: 0.8349 (t) cc_final: 0.8048 (p) REVERT: D 46 LEU cc_start: 0.8454 (tp) cc_final: 0.8246 (tt) REVERT: E 425 GLU cc_start: 0.7860 (tt0) cc_final: 0.7584 (tt0) REVERT: F 82 ASN cc_start: 0.8396 (m-40) cc_final: 0.8070 (m-40) REVERT: F 89 VAL cc_start: 0.8351 (t) cc_final: 0.8038 (p) REVERT: I 313 VAL cc_start: 0.8623 (m) cc_final: 0.8393 (t) REVERT: I 425 GLU cc_start: 0.7891 (tt0) cc_final: 0.7601 (tt0) REVERT: J 82 ASN cc_start: 0.8335 (m-40) cc_final: 0.8003 (m-40) REVERT: J 89 VAL cc_start: 0.8333 (t) cc_final: 0.8062 (p) outliers start: 58 outliers final: 42 residues processed: 436 average time/residue: 1.3461 time to fit residues: 659.5043 Evaluate side-chains 441 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP 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 D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 399 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 172 LYS Chi-restraints excluded: chain I residue 215 VAL 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 399 ASP Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 168 HIS B 226 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN E 385 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19520 Z= 0.324 Angle : 0.662 11.502 26480 Z= 0.346 Chirality : 0.048 0.150 2904 Planarity : 0.005 0.052 3408 Dihedral : 5.838 38.379 2940 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.94 % Allowed : 15.06 % 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: -0.97 (0.16), residues: 2440 helix: -2.00 (0.75), residues: 24 sheet: 0.63 (0.18), residues: 900 loop : -1.52 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 178 HIS 0.007 0.001 HIS A 336 PHE 0.023 0.003 PHE B 205 TYR 0.018 0.002 TYR B 281 ARG 0.008 0.001 ARG B 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 463 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 401 time to evaluate : 2.127 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6387 (m) cc_final: 0.6139 (m) REVERT: A 234 ASN cc_start: 0.7500 (t0) cc_final: 0.7261 (t0) REVERT: A 425 GLU cc_start: 0.7875 (tt0) cc_final: 0.7507 (tt0) REVERT: A 432 GLU cc_start: 0.7211 (mp0) cc_final: 0.6941 (mp0) REVERT: A 466 LEU cc_start: 0.8648 (mp) cc_final: 0.8447 (mt) REVERT: H 89 VAL cc_start: 0.8444 (t) cc_final: 0.8136 (p) REVERT: B 234 ASN cc_start: 0.7567 (t0) cc_final: 0.7237 (t0) REVERT: B 247 THR cc_start: 0.8300 (p) cc_final: 0.8087 (t) REVERT: C 82 ASN cc_start: 0.8455 (m-40) cc_final: 0.8139 (m-40) REVERT: C 89 VAL cc_start: 0.8374 (t) cc_final: 0.8073 (p) REVERT: E 140 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7969 (tp) REVERT: F 82 ASN cc_start: 0.8433 (m-40) cc_final: 0.8078 (m-40) REVERT: F 89 VAL cc_start: 0.8368 (t) cc_final: 0.8059 (p) REVERT: I 140 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8013 (tp) REVERT: I 313 VAL cc_start: 0.8614 (m) cc_final: 0.8392 (t) REVERT: I 425 GLU cc_start: 0.7935 (tt0) cc_final: 0.7651 (tt0) REVERT: J 82 ASN cc_start: 0.8428 (m-40) cc_final: 0.8061 (m-40) REVERT: J 89 VAL cc_start: 0.8345 (t) cc_final: 0.8071 (p) outliers start: 62 outliers final: 46 residues processed: 432 average time/residue: 1.3284 time to fit residues: 648.2933 Evaluate side-chains 448 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 400 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 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 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 172 LYS 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 390 LEU Chi-restraints excluded: chain I residue 421 CYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.2980 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 226 GLN B 294 ASN D 37 GLN E 294 ASN E 385 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19520 Z= 0.192 Angle : 0.596 10.816 26480 Z= 0.311 Chirality : 0.046 0.167 2904 Planarity : 0.004 0.049 3408 Dihedral : 5.522 37.476 2940 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.46 % Allowed : 15.96 % Favored : 81.58 % 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 (0.17), residues: 2440 helix: -1.94 (0.78), residues: 24 sheet: 0.47 (0.18), residues: 920 loop : -1.36 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 178 HIS 0.005 0.001 HIS A 336 PHE 0.017 0.002 PHE A 410 TYR 0.016 0.001 TYR H 91 ARG 0.010 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 460 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ASN cc_start: 0.7463 (t0) cc_final: 0.7194 (t0) REVERT: A 391 GLN cc_start: 0.8361 (pt0) cc_final: 0.8051 (pt0) REVERT: A 432 GLU cc_start: 0.7169 (mp0) cc_final: 0.6929 (mp0) REVERT: H 82 ASN cc_start: 0.8381 (m-40) cc_final: 0.7973 (m-40) REVERT: H 89 VAL cc_start: 0.8413 (t) cc_final: 0.8127 (p) REVERT: B 432 GLU cc_start: 0.7190 (mp0) cc_final: 0.6847 (mp0) REVERT: C 82 ASN cc_start: 0.8390 (m-40) cc_final: 0.8118 (m-40) REVERT: C 89 VAL cc_start: 0.8329 (t) cc_final: 0.8035 (p) REVERT: E 435 GLU cc_start: 0.6672 (pt0) cc_final: 0.6444 (pt0) REVERT: F 82 ASN cc_start: 0.8384 (m-40) cc_final: 0.8055 (m-40) REVERT: F 89 VAL cc_start: 0.8322 (t) cc_final: 0.8034 (p) REVERT: I 172 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: I 313 VAL cc_start: 0.8589 (m) cc_final: 0.8368 (t) REVERT: I 431 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7294 (mppt) REVERT: I 432 GLU cc_start: 0.7198 (mp0) cc_final: 0.6970 (mp0) REVERT: J 82 ASN cc_start: 0.8346 (m-40) cc_final: 0.8016 (m-40) REVERT: J 89 VAL cc_start: 0.8316 (t) cc_final: 0.8059 (p) outliers start: 52 outliers final: 43 residues processed: 432 average time/residue: 1.3975 time to fit residues: 684.8800 Evaluate side-chains 440 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 395 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP 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 D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 172 LYS 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 J residue 53 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.0030 chunk 116 optimal weight: 4.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- 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 226 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN E 385 ASN G 37 GLN I 245 ASN I 294 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19520 Z= 0.425 Angle : 0.723 11.633 26480 Z= 0.377 Chirality : 0.050 0.198 2904 Planarity : 0.005 0.068 3408 Dihedral : 6.035 38.706 2940 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.60 % Allowed : 16.15 % Favored : 81.25 % 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: -0.91 (0.16), residues: 2440 helix: -2.14 (0.72), residues: 24 sheet: 0.71 (0.18), residues: 896 loop : -1.49 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 178 HIS 0.007 0.002 HIS A 336 PHE 0.027 0.003 PHE B 205 TYR 0.022 0.002 TYR E 281 ARG 0.011 0.001 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 457 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 402 time to evaluate : 2.163 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.6360 (m) cc_final: 0.6107 (m) REVERT: A 234 ASN cc_start: 0.7517 (t0) cc_final: 0.7273 (t0) REVERT: A 432 GLU cc_start: 0.7247 (mp0) cc_final: 0.6974 (mp0) REVERT: H 89 VAL cc_start: 0.8462 (t) cc_final: 0.8138 (p) REVERT: B 234 ASN cc_start: 0.7593 (t0) cc_final: 0.7233 (t0) REVERT: C 82 ASN cc_start: 0.8474 (m-40) cc_final: 0.8155 (m-40) REVERT: C 89 VAL cc_start: 0.8400 (t) cc_final: 0.8093 (p) REVERT: E 140 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7964 (tp) REVERT: F 82 ASN cc_start: 0.8442 (m-40) cc_final: 0.8067 (m-40) REVERT: F 89 VAL cc_start: 0.8406 (t) cc_final: 0.8086 (p) REVERT: I 140 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (tp) REVERT: I 307 ILE cc_start: 0.8604 (mm) cc_final: 0.8403 (mp) REVERT: I 313 VAL cc_start: 0.8611 (m) cc_final: 0.8399 (t) REVERT: J 82 ASN cc_start: 0.8456 (m-40) cc_final: 0.8073 (m-40) REVERT: J 89 VAL cc_start: 0.8381 (t) cc_final: 0.8096 (p) outliers start: 55 outliers final: 46 residues processed: 426 average time/residue: 1.3083 time to fit residues: 629.2832 Evaluate side-chains 444 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 396 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 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 318 CYS Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 421 CYS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain I residue 128 LYS Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 162 GLU Chi-restraints excluded: chain I residue 172 LYS 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 421 CYS Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 226 GLN B 294 ASN D 37 GLN E 226 GLN E 294 ASN E 385 ASN G 37 GLN I 294 ASN K 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099959 restraints weight = 24747.683| |-----------------------------------------------------------------------------| 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: 0.2994 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2558 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: