Starting phenix.real_space_refine on Sun Aug 24 22:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.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 { model { file = "/net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcn_34659/08_2025/8hcn_34659.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 14898 2.51 5 N 4158 2.21 5 O 4395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23568 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "B" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "C" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "D" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Chain: "E" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "F" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "G" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "H" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Chain: "I" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 776 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "J" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 800 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "K" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4224 Classifications: {'peptide': 566} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 537} Chain: "L" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2056 Classifications: {'peptide': 264} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 245} Time building chain proxies: 6.20, per 1000 atoms: 0.26 Number of scatterers: 23568 At special positions: 0 Unit cell: (149.604, 151.248, 90.42, 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 117 16.00 O 4395 8.00 N 4158 7.00 C 14898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5634 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 48 sheets defined 30.0% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.616A pdb=" N VAL B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 140 through 150 removed outlier: 3.997A pdb=" N GLU C 144 " --> pdb=" O PRO C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.654A pdb=" N ALA C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 removed outlier: 4.257A pdb=" N TYR C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.860A pdb=" N LEU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.901A pdb=" N THR C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.622A pdb=" N MET C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.806A pdb=" N ASP C 346 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 386 removed outlier: 3.522A pdb=" N ARG C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 477 through 479 No H-bonds generated for 'chain 'C' and resid 477 through 479' Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 219 through 225 removed outlier: 6.968A pdb=" N LEU D 223 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR D 224 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 225 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 263 Proline residue: D 259 - end of helix Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 4 through 27 Processing helix chain 'E' and resid 31 through 50 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.652A pdb=" N VAL F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 14 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 140 through 150 removed outlier: 4.025A pdb=" N GLU G 144 " --> pdb=" O PRO G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 168 removed outlier: 3.625A pdb=" N ALA G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 removed outlier: 4.149A pdb=" N TYR G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G 185 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 212 removed outlier: 3.867A pdb=" N LEU G 205 " --> pdb=" O GLN G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 240 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 282 through 290 Processing helix chain 'G' and resid 298 through 302 removed outlier: 3.901A pdb=" N THR G 301 " --> pdb=" O THR G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 320 removed outlier: 3.624A pdb=" N MET G 315 " --> pdb=" O GLU G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 333 Processing helix chain 'G' and resid 338 through 351 removed outlier: 3.828A pdb=" N ASP G 346 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 347 " --> pdb=" O ALA G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 386 removed outlier: 3.548A pdb=" N ARG G 373 " --> pdb=" O GLU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 409 through 415 Processing helix chain 'G' and resid 436 through 440 removed outlier: 3.572A pdb=" N PHE G 440 " --> pdb=" O PRO G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 479 No H-bonds generated for 'chain 'G' and resid 477 through 479' Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 493 through 500 Processing helix chain 'G' and resid 500 through 506 Processing helix chain 'G' and resid 521 through 525 Processing helix chain 'H' and resid 207 through 218 Processing helix chain 'H' and resid 219 through 225 removed outlier: 6.972A pdb=" N LEU H 223 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR H 224 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA H 225 " --> pdb=" O GLY H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 263 Proline residue: H 259 - end of helix Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'I' and resid 4 through 27 Processing helix chain 'I' and resid 31 through 50 Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 67 through 69 No H-bonds generated for 'chain 'I' and resid 67 through 69' Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.598A pdb=" N VAL J 45 " --> pdb=" O PHE J 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.651A pdb=" N CYS K 65 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 150 removed outlier: 4.041A pdb=" N GLU K 144 " --> pdb=" O PRO K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 168 removed outlier: 3.679A pdb=" N ALA K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 185 removed outlier: 4.126A pdb=" N TYR K 176 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP K 185 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 212 removed outlier: 3.876A pdb=" N LEU K 205 " --> pdb=" O GLN K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 240 Processing helix chain 'K' and resid 255 through 264 Processing helix chain 'K' and resid 282 through 290 Processing helix chain 'K' and resid 298 through 302 removed outlier: 3.928A pdb=" N THR K 301 " --> pdb=" O THR K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 320 removed outlier: 3.630A pdb=" N MET K 315 " --> pdb=" O GLU K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 333 Processing helix chain 'K' and resid 338 through 351 removed outlier: 3.811A pdb=" N ASP K 346 " --> pdb=" O ILE K 342 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 386 removed outlier: 3.537A pdb=" N ARG K 373 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'K' and resid 409 through 415 Processing helix chain 'K' and resid 436 through 440 Processing helix chain 'K' and resid 477 through 479 No H-bonds generated for 'chain 'K' and resid 477 through 479' Processing helix chain 'K' and resid 480 through 487 Processing helix chain 'K' and resid 493 through 499 Processing helix chain 'K' and resid 500 through 505 Processing helix chain 'L' and resid 207 through 218 Processing helix chain 'L' and resid 219 through 225 removed outlier: 6.978A pdb=" N LEU L 223 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR L 224 " --> pdb=" O LEU L 221 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA L 225 " --> pdb=" O GLY L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 263 Proline residue: L 259 - end of helix Processing helix chain 'L' and resid 269 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.400A pdb=" N LEU A 64 " --> pdb=" O ILE A 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 86 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB1, first strand: chain 'C' and resid 34 through 35 removed outlier: 6.775A pdb=" N ASP C 34 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP C 85 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 82 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C 74 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA C 84 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN C 72 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 69 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 97 removed outlier: 6.667A pdb=" N GLY C 87 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 96 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP C 85 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 82 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C 74 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA C 84 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN C 72 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA C 128 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 447 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 136 removed outlier: 6.424A pdb=" N GLY C 130 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 155 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP C 132 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLY C 157 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N HIS C 134 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 215 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL C 243 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 268 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 492 removed outlier: 5.896A pdb=" N THR C 490 " --> pdb=" O ALA C 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 534 through 535 Processing sheet with id=AB7, first strand: chain 'D' and resid 27 through 36 removed outlier: 4.997A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA D 24 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 30 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS D 22 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA D 99 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE D 131 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 101 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR D 133 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN D 103 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS D 135 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 105 " --> pdb=" O HIS D 135 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 172 " --> pdb=" O PRO D 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 52 through 55 removed outlier: 6.926A pdb=" N THR D 81 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 116 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 83 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 120 " --> pdb=" O CYS D 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 55 removed outlier: 6.926A pdb=" N THR D 81 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 116 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 83 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 64 through 65 removed outlier: 7.405A pdb=" N LEU E 64 " --> pdb=" O ILE E 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 86 Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'F' and resid 34 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC7, first strand: chain 'G' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'G' and resid 34 through 35 removed outlier: 6.784A pdb=" N ASP G 34 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASP G 85 " --> pdb=" O ASP G 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL G 76 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 82 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU G 74 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA G 84 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 72 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL G 69 " --> pdb=" O ILE G 119 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 92 through 97 removed outlier: 5.012A pdb=" N ILE G 93 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS G 89 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL G 76 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL G 82 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU G 74 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA G 84 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 72 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA G 128 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL G 447 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 99 through 100 Processing sheet with id=AD2, first strand: chain 'G' and resid 130 through 136 removed outlier: 6.406A pdb=" N GLY G 130 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL G 155 " --> pdb=" O GLY G 130 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP G 132 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLY G 157 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N HIS G 134 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 215 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 243 " --> pdb=" O HIS G 269 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE G 268 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 489 through 492 Processing sheet with id=AD4, first strand: chain 'G' and resid 534 through 535 Processing sheet with id=AD5, first strand: chain 'H' and resid 27 through 36 removed outlier: 4.994A pdb=" N THR H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA H 24 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU H 30 " --> pdb=" O HIS H 22 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS H 22 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA H 99 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE H 131 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL H 101 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR H 133 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN H 103 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS H 135 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU H 105 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL H 172 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.930A pdb=" N THR H 81 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU H 116 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE H 83 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 120 " --> pdb=" O CYS H 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 52 through 55 removed outlier: 6.930A pdb=" N THR H 81 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU H 116 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE H 83 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 64 through 65 removed outlier: 7.434A pdb=" N LEU I 64 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 79 through 86 Processing sheet with id=AE1, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 Processing sheet with id=AE3, first strand: chain 'J' and resid 89 through 90 Processing sheet with id=AE4, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.768A pdb=" N ASP K 34 " --> pdb=" O LYS K 83 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASP K 85 " --> pdb=" O ASP K 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 80 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 76 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL K 82 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU K 74 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA K 84 " --> pdb=" O ASN K 72 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN K 72 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL K 69 " --> pdb=" O ILE K 119 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 92 through 97 removed outlier: 6.671A pdb=" N GLY K 87 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE K 96 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP K 85 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 80 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 76 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL K 82 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU K 74 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA K 84 " --> pdb=" O ASN K 72 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN K 72 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA K 128 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL K 447 " --> pdb=" O ALA K 454 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 99 through 100 Processing sheet with id=AE7, first strand: chain 'K' and resid 130 through 136 removed outlier: 6.415A pdb=" N GLY K 130 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL K 155 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP K 132 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY K 157 " --> pdb=" O ASP K 132 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS K 134 " --> pdb=" O GLY K 157 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY K 215 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL K 243 " --> pdb=" O HIS K 269 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE K 268 " --> pdb=" O LEU K 294 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 130 through 136 removed outlier: 6.415A pdb=" N GLY K 130 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL K 155 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP K 132 " --> pdb=" O VAL K 155 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY K 157 " --> pdb=" O ASP K 132 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS K 134 " --> pdb=" O GLY K 157 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE K 191 " --> pdb=" O PHE K 491 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR K 490 " --> pdb=" O ALA K 512 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 534 through 535 Processing sheet with id=AF1, first strand: chain 'L' and resid 27 through 36 removed outlier: 4.995A pdb=" N THR L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA L 24 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU L 30 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS L 22 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA L 99 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE L 131 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL L 101 " --> pdb=" O PHE L 131 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR L 133 " --> pdb=" O VAL L 101 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN L 103 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS L 135 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU L 105 " --> pdb=" O HIS L 135 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL L 172 " --> pdb=" O PRO L 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 52 through 55 removed outlier: 6.944A pdb=" N THR L 81 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU L 116 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 83 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA L 120 " --> pdb=" O CYS L 149 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 52 through 55 removed outlier: 6.944A pdb=" N THR L 81 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU L 116 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 83 " --> pdb=" O LEU L 116 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2577 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: 5.73 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8017 1.34 - 1.46: 4497 1.46 - 1.57: 11375 1.57 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 24078 Sorted by residual: bond pdb=" C LYS G 443 " pdb=" O LYS G 443 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.73e+00 bond pdb=" C ASN K 299 " pdb=" N PRO K 300 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.53e-01 bond pdb=" CA ASP G 25 " pdb=" CB ASP G 25 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.53e-01 bond pdb=" C ASN G 299 " pdb=" N PRO G 300 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.46e-01 bond pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.69e-02 3.50e+03 7.26e-01 ... (remaining 24073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 32183 1.56 - 3.13: 503 3.13 - 4.69: 68 4.69 - 6.25: 24 6.25 - 7.82: 9 Bond angle restraints: 32787 Sorted by residual: angle pdb=" N THR G 467 " pdb=" CA THR G 467 " pdb=" C THR G 467 " ideal model delta sigma weight residual 109.81 117.63 -7.82 2.21e+00 2.05e-01 1.25e+01 angle pdb=" N THR K 467 " pdb=" CA THR K 467 " pdb=" C THR K 467 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N THR C 467 " pdb=" CA THR C 467 " pdb=" C THR C 467 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 angle pdb=" C ALA G 24 " pdb=" N ASP G 25 " pdb=" CA ASP G 25 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C ALA C 24 " pdb=" N ASP C 25 " pdb=" CA ASP C 25 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 ... (remaining 32782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 13164 17.41 - 34.81: 994 34.81 - 52.22: 149 52.22 - 69.63: 20 69.63 - 87.03: 25 Dihedral angle restraints: 14352 sinusoidal: 5577 harmonic: 8775 Sorted by residual: dihedral pdb=" CA TRP C 435 " pdb=" C TRP C 435 " pdb=" N SER C 436 " pdb=" CA SER C 436 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP K 435 " pdb=" C TRP K 435 " pdb=" N SER K 436 " pdb=" CA SER K 436 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP G 360 " pdb=" C ASP G 360 " pdb=" N SER G 361 " pdb=" CA SER G 361 " ideal model delta harmonic sigma weight residual 180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2352 0.033 - 0.066: 919 0.066 - 0.099: 306 0.099 - 0.132: 181 0.132 - 0.165: 7 Chirality restraints: 3765 Sorted by residual: chirality pdb=" CA ASP C 25 " pdb=" N ASP C 25 " pdb=" C ASP C 25 " pdb=" CB ASP C 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA ASP K 25 " pdb=" N ASP K 25 " pdb=" C ASP K 25 " pdb=" CB ASP K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ASP G 25 " pdb=" N ASP G 25 " pdb=" C ASP G 25 " pdb=" CB ASP G 25 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 3762 not shown) Planarity restraints: 4296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.019 2.00e-02 2.50e+03 1.72e-02 7.36e+00 pdb=" CG TRP D 145 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 145 " -0.020 2.00e-02 2.50e+03 1.70e-02 7.24e+00 pdb=" CG TRP L 145 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP L 145 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP L 145 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 145 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 145 " 0.020 2.00e-02 2.50e+03 1.70e-02 7.21e+00 pdb=" CG TRP H 145 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP H 145 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 145 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 145 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 145 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 4293 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2424 2.75 - 3.29: 23397 3.29 - 3.82: 41712 3.82 - 4.36: 52879 4.36 - 4.90: 89843 Nonbonded interactions: 210255 Sorted by model distance: nonbonded pdb=" OG SER K 297 " pdb=" OE2 GLU K 345 " model vdw 2.209 3.040 nonbonded pdb=" OG SER G 297 " pdb=" OE2 GLU G 345 " model vdw 2.212 3.040 nonbonded pdb=" O LEU C 566 " pdb=" NH1 ARG E 23 " model vdw 2.215 3.120 nonbonded pdb=" O LEU G 566 " pdb=" NH1 ARG I 23 " model vdw 2.222 3.120 nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 67 " model vdw 2.231 3.040 ... (remaining 210250 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.900 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.003 0.036 24078 Z= 0.131 Angle : 0.511 7.816 32787 Z= 0.262 Chirality : 0.044 0.165 3765 Planarity : 0.004 0.040 4296 Dihedral : 12.712 87.035 8718 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3075 helix: 1.72 (0.20), residues: 744 sheet: 0.01 (0.19), residues: 714 loop : -0.49 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 338 TYR 0.007 0.001 TYR D 204 PHE 0.007 0.001 PHE H 238 TRP 0.047 0.002 TRP D 145 HIS 0.004 0.001 HIS G 415 Details of bonding type rmsd covalent geometry : bond 0.00297 (24078) covalent geometry : angle 0.51133 (32787) hydrogen bonds : bond 0.14670 ( 934) hydrogen bonds : angle 7.43741 ( 2577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.8769 (mp0) cc_final: 0.7947 (mp0) REVERT: A 45 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 31 ASP cc_start: 0.8186 (p0) cc_final: 0.7892 (p0) REVERT: B 52 ASP cc_start: 0.8708 (t0) cc_final: 0.8427 (t0) REVERT: B 55 GLN cc_start: 0.8603 (tt0) cc_final: 0.8294 (tt0) REVERT: B 78 GLU cc_start: 0.8407 (tt0) cc_final: 0.8091 (tm-30) REVERT: C 11 ASP cc_start: 0.8342 (m-30) cc_final: 0.8042 (m-30) REVERT: D 50 GLU cc_start: 0.8706 (pm20) cc_final: 0.8458 (pm20) REVERT: D 68 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 146 ASP cc_start: 0.8093 (t70) cc_final: 0.7610 (t0) REVERT: D 175 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 264 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8349 (mmtm) REVERT: E 2 GLU cc_start: 0.8710 (mp0) cc_final: 0.7701 (mp0) REVERT: E 45 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 27 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7917 (mp0) REVERT: F 31 ASP cc_start: 0.8272 (p0) cc_final: 0.7936 (p0) REVERT: F 55 GLN cc_start: 0.8610 (tt0) cc_final: 0.8324 (tt0) REVERT: G 11 ASP cc_start: 0.8352 (m-30) cc_final: 0.8079 (m-30) REVERT: G 117 GLU cc_start: 0.7833 (tp30) cc_final: 0.7623 (tp30) REVERT: H 68 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 146 ASP cc_start: 0.8135 (t70) cc_final: 0.7403 (p0) REVERT: H 169 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8000 (mt-10) REVERT: H 175 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8263 (tm-30) REVERT: H 264 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8413 (mmtm) REVERT: I 1 MET cc_start: 0.8697 (mtp) cc_final: 0.8423 (mtm) REVERT: I 2 GLU cc_start: 0.8892 (mp0) cc_final: 0.7702 (mp0) REVERT: I 45 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7823 (mm-30) REVERT: I 65 THR cc_start: 0.8850 (p) cc_final: 0.8589 (p) REVERT: I 67 GLU cc_start: 0.8185 (pm20) cc_final: 0.7935 (pm20) REVERT: J 27 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7967 (mp0) REVERT: J 31 ASP cc_start: 0.8199 (p0) cc_final: 0.7878 (p0) REVERT: J 50 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8676 (mmtm) REVERT: J 52 ASP cc_start: 0.8682 (t0) cc_final: 0.8433 (t0) REVERT: J 55 GLN cc_start: 0.8863 (tt0) cc_final: 0.8650 (tt0) REVERT: K 11 ASP cc_start: 0.8331 (m-30) cc_final: 0.8039 (m-30) REVERT: K 132 ASP cc_start: 0.8261 (t0) cc_final: 0.8049 (t0) REVERT: L 50 GLU cc_start: 0.8747 (pm20) cc_final: 0.8470 (pm20) REVERT: L 146 ASP cc_start: 0.8142 (t70) cc_final: 0.7364 (p0) REVERT: L 169 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7981 (mt-10) REVERT: L 175 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8230 (tm-30) REVERT: L 264 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8544 (mptp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.8635 time to fit residues: 334.1375 Evaluate side-chains 255 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 201 GLN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 349 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 531 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 247 GLN F 75 GLN G 201 GLN G 299 ASN G 349 HIS ** G 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 ASN H 22 HIS H 185 GLN H 247 GLN J 55 GLN J 75 GLN K 201 GLN K 299 ASN K 349 HIS K 499 ASN K 521 GLN L 22 HIS L 161 HIS L 185 GLN L 247 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.071076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055017 restraints weight = 51307.822| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.78 r_work: 0.2618 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24078 Z= 0.159 Angle : 0.562 8.326 32787 Z= 0.286 Chirality : 0.044 0.163 3765 Planarity : 0.004 0.038 4296 Dihedral : 4.289 39.255 3318 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.05 % Allowed : 6.44 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3075 helix: 1.84 (0.20), residues: 753 sheet: -0.10 (0.19), residues: 732 loop : -0.36 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 23 TYR 0.010 0.001 TYR H 55 PHE 0.008 0.001 PHE C 565 TRP 0.030 0.002 TRP H 145 HIS 0.005 0.001 HIS G 472 Details of bonding type rmsd covalent geometry : bond 0.00360 (24078) covalent geometry : angle 0.56164 (32787) hydrogen bonds : bond 0.03717 ( 934) hydrogen bonds : angle 5.67417 ( 2577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 1.219 Fit side-chains REVERT: B 9 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8722 (ptmm) REVERT: B 27 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7689 (mp0) REVERT: B 31 ASP cc_start: 0.8579 (p0) cc_final: 0.8301 (p0) REVERT: B 52 ASP cc_start: 0.8652 (t0) cc_final: 0.8044 (t0) REVERT: B 55 GLN cc_start: 0.9106 (tt0) cc_final: 0.8707 (tt0) REVERT: B 78 GLU cc_start: 0.8788 (tt0) cc_final: 0.8213 (tm-30) REVERT: C 11 ASP cc_start: 0.8734 (m-30) cc_final: 0.8408 (m-30) REVERT: D 146 ASP cc_start: 0.8273 (t70) cc_final: 0.7838 (t0) REVERT: D 175 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 2 GLU cc_start: 0.8954 (mp0) cc_final: 0.7843 (mp0) REVERT: F 27 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7853 (mp0) REVERT: F 31 ASP cc_start: 0.8634 (p0) cc_final: 0.8287 (p0) REVERT: F 52 ASP cc_start: 0.8723 (t0) cc_final: 0.8472 (t0) REVERT: F 55 GLN cc_start: 0.9097 (tt0) cc_final: 0.8787 (tt0) REVERT: F 80 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: G 11 ASP cc_start: 0.8732 (m-30) cc_final: 0.8440 (m-30) REVERT: G 117 GLU cc_start: 0.8424 (tp30) cc_final: 0.7978 (tp30) REVERT: H 146 ASP cc_start: 0.8288 (t70) cc_final: 0.7443 (p0) REVERT: H 175 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8333 (tm-30) REVERT: I 65 THR cc_start: 0.8716 (p) cc_final: 0.8452 (p) REVERT: I 67 GLU cc_start: 0.8670 (pm20) cc_final: 0.8330 (pm20) REVERT: J 27 GLU cc_start: 0.8495 (mt-10) cc_final: 0.7778 (mp0) REVERT: J 31 ASP cc_start: 0.8574 (p0) cc_final: 0.8249 (p0) REVERT: J 52 ASP cc_start: 0.8657 (t0) cc_final: 0.8350 (t0) REVERT: J 55 GLN cc_start: 0.9141 (tt0) cc_final: 0.8831 (tt0) REVERT: J 80 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: K 11 ASP cc_start: 0.8705 (m-30) cc_final: 0.8318 (m-30) REVERT: L 146 ASP cc_start: 0.8249 (t70) cc_final: 0.7400 (p0) REVERT: L 175 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 26 outliers final: 6 residues processed: 272 average time/residue: 0.7626 time to fit residues: 234.9317 Evaluate side-chains 270 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 261 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 22 HIS Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 240 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN G 384 GLN H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.054020 restraints weight = 51355.174| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.78 r_work: 0.2593 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24078 Z= 0.203 Angle : 0.562 7.900 32787 Z= 0.284 Chirality : 0.045 0.166 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.345 40.834 3318 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.13 % Allowed : 8.25 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3075 helix: 1.78 (0.20), residues: 756 sheet: 0.05 (0.19), residues: 723 loop : -0.29 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 258 TYR 0.011 0.001 TYR D 204 PHE 0.010 0.001 PHE H 21 TRP 0.027 0.001 TRP H 145 HIS 0.010 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00465 (24078) covalent geometry : angle 0.56198 (32787) hydrogen bonds : bond 0.03596 ( 934) hydrogen bonds : angle 5.35358 ( 2577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.954 Fit side-chains REVERT: B 9 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8736 (ptmm) REVERT: B 27 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7720 (mp0) REVERT: B 31 ASP cc_start: 0.8591 (p0) cc_final: 0.8257 (p0) REVERT: B 52 ASP cc_start: 0.8690 (t0) cc_final: 0.8044 (t0) REVERT: B 55 GLN cc_start: 0.9091 (tt0) cc_final: 0.8660 (tt0) REVERT: B 78 GLU cc_start: 0.8814 (tt0) cc_final: 0.8205 (tm-30) REVERT: C 11 ASP cc_start: 0.8730 (m-30) cc_final: 0.8384 (m-30) REVERT: C 117 GLU cc_start: 0.8443 (tp30) cc_final: 0.8102 (tp30) REVERT: C 334 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7191 (tp30) REVERT: C 508 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8120 (mmm160) REVERT: D 146 ASP cc_start: 0.8302 (t70) cc_final: 0.7904 (t0) REVERT: D 175 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8369 (tm-30) REVERT: E 2 GLU cc_start: 0.8985 (mp0) cc_final: 0.7893 (mp0) REVERT: F 27 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7867 (mp0) REVERT: F 31 ASP cc_start: 0.8615 (p0) cc_final: 0.8320 (p0) REVERT: F 52 ASP cc_start: 0.8724 (t0) cc_final: 0.8368 (t0) REVERT: F 55 GLN cc_start: 0.9113 (tt0) cc_final: 0.8773 (tt0) REVERT: F 80 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: G 11 ASP cc_start: 0.8721 (m-30) cc_final: 0.8421 (m-30) REVERT: G 117 GLU cc_start: 0.8431 (tp30) cc_final: 0.7966 (tp30) REVERT: H 146 ASP cc_start: 0.8277 (t70) cc_final: 0.7434 (p0) REVERT: H 175 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8380 (tm-30) REVERT: I 2 GLU cc_start: 0.9075 (mp0) cc_final: 0.7845 (mp0) REVERT: I 7 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8338 (mt-10) REVERT: I 65 THR cc_start: 0.8752 (p) cc_final: 0.8505 (p) REVERT: I 67 GLU cc_start: 0.8672 (pm20) cc_final: 0.8335 (pm20) REVERT: J 27 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7787 (mp0) REVERT: J 31 ASP cc_start: 0.8544 (p0) cc_final: 0.8237 (p0) REVERT: J 52 ASP cc_start: 0.8665 (t0) cc_final: 0.8324 (t0) REVERT: J 55 GLN cc_start: 0.9164 (tt0) cc_final: 0.8853 (tt0) REVERT: J 80 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8235 (mm-30) REVERT: K 11 ASP cc_start: 0.8701 (m-30) cc_final: 0.8323 (m-30) REVERT: L 146 ASP cc_start: 0.8248 (t70) cc_final: 0.7393 (p0) REVERT: L 175 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8325 (tm-30) REVERT: L 186 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7530 (mm-30) outliers start: 28 outliers final: 7 residues processed: 285 average time/residue: 0.8225 time to fit residues: 263.2578 Evaluate side-chains 269 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 149 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 296 optimal weight: 9.9990 chunk 286 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN H 22 HIS H 247 GLN I 97 ASN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055683 restraints weight = 50850.790| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.77 r_work: 0.2636 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24078 Z= 0.122 Angle : 0.525 7.561 32787 Z= 0.266 Chirality : 0.044 0.161 3765 Planarity : 0.004 0.035 4296 Dihedral : 4.222 40.858 3318 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.01 % Allowed : 9.66 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3075 helix: 1.67 (0.20), residues: 777 sheet: -0.04 (0.19), residues: 729 loop : -0.35 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 6 TYR 0.010 0.001 TYR K 176 PHE 0.006 0.001 PHE H 238 TRP 0.021 0.001 TRP H 145 HIS 0.006 0.001 HIS K 134 Details of bonding type rmsd covalent geometry : bond 0.00278 (24078) covalent geometry : angle 0.52472 (32787) hydrogen bonds : bond 0.03086 ( 934) hydrogen bonds : angle 5.07202 ( 2577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.995 Fit side-chains REVERT: B 9 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8740 (ptmm) REVERT: B 27 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7724 (mp0) REVERT: B 31 ASP cc_start: 0.8551 (p0) cc_final: 0.8310 (p0) REVERT: B 52 ASP cc_start: 0.8613 (t0) cc_final: 0.8285 (t0) REVERT: B 55 GLN cc_start: 0.9107 (tt0) cc_final: 0.8755 (tt0) REVERT: B 78 GLU cc_start: 0.8796 (tt0) cc_final: 0.8194 (tm-30) REVERT: C 11 ASP cc_start: 0.8726 (m-30) cc_final: 0.8389 (m-30) REVERT: C 117 GLU cc_start: 0.8425 (tp30) cc_final: 0.8044 (tp30) REVERT: C 334 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7210 (tp30) REVERT: D 146 ASP cc_start: 0.8242 (t70) cc_final: 0.7860 (t0) REVERT: D 175 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8393 (tm-30) REVERT: F 27 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7841 (mp0) REVERT: F 31 ASP cc_start: 0.8597 (p0) cc_final: 0.8318 (p0) REVERT: F 52 ASP cc_start: 0.8691 (t0) cc_final: 0.8294 (t0) REVERT: F 55 GLN cc_start: 0.9118 (tt0) cc_final: 0.8784 (tt0) REVERT: F 80 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: G 11 ASP cc_start: 0.8735 (m-30) cc_final: 0.8436 (m-30) REVERT: G 117 GLU cc_start: 0.8402 (tp30) cc_final: 0.7918 (tp30) REVERT: H 146 ASP cc_start: 0.8238 (t70) cc_final: 0.7412 (p0) REVERT: H 175 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8372 (tm-30) REVERT: I 2 GLU cc_start: 0.9053 (mp0) cc_final: 0.7810 (mp0) REVERT: I 65 THR cc_start: 0.8711 (p) cc_final: 0.8454 (p) REVERT: I 67 GLU cc_start: 0.8678 (pm20) cc_final: 0.8335 (pm20) REVERT: J 27 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7780 (mp0) REVERT: J 31 ASP cc_start: 0.8511 (p0) cc_final: 0.8219 (p0) REVERT: J 52 ASP cc_start: 0.8601 (t0) cc_final: 0.8318 (t0) REVERT: J 55 GLN cc_start: 0.9156 (tt0) cc_final: 0.8828 (tt0) REVERT: J 80 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: K 11 ASP cc_start: 0.8709 (m-30) cc_final: 0.8314 (m-30) REVERT: L 146 ASP cc_start: 0.8236 (t70) cc_final: 0.7426 (p0) REVERT: L 175 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8277 (tm-30) outliers start: 25 outliers final: 6 residues processed: 276 average time/residue: 0.7742 time to fit residues: 242.0191 Evaluate side-chains 281 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN F 12 GLN H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053418 restraints weight = 51240.174| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.76 r_work: 0.2579 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24078 Z= 0.244 Angle : 0.577 7.911 32787 Z= 0.290 Chirality : 0.045 0.164 3765 Planarity : 0.004 0.039 4296 Dihedral : 4.355 40.781 3318 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.21 % Allowed : 10.67 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3075 helix: 1.75 (0.20), residues: 753 sheet: 0.05 (0.19), residues: 723 loop : -0.29 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.013 0.001 TYR K 176 PHE 0.026 0.001 PHE H 238 TRP 0.024 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00565 (24078) covalent geometry : angle 0.57719 (32787) hydrogen bonds : bond 0.03603 ( 934) hydrogen bonds : angle 5.16689 ( 2577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.938 Fit side-chains REVERT: B 9 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (ptmm) REVERT: B 27 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7737 (mp0) REVERT: B 31 ASP cc_start: 0.8560 (p0) cc_final: 0.8269 (p0) REVERT: B 52 ASP cc_start: 0.8677 (t0) cc_final: 0.8333 (t0) REVERT: B 55 GLN cc_start: 0.9083 (tt0) cc_final: 0.8753 (tt0) REVERT: B 80 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 11 ASP cc_start: 0.8716 (m-30) cc_final: 0.8367 (m-30) REVERT: C 117 GLU cc_start: 0.8454 (tp30) cc_final: 0.7997 (tp30) REVERT: D 146 ASP cc_start: 0.8287 (t70) cc_final: 0.7916 (t0) REVERT: D 175 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8448 (tm-30) REVERT: E 2 GLU cc_start: 0.9025 (mp0) cc_final: 0.7919 (mp0) REVERT: F 27 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7860 (mp0) REVERT: F 31 ASP cc_start: 0.8592 (p0) cc_final: 0.8352 (p0) REVERT: F 52 ASP cc_start: 0.8770 (t0) cc_final: 0.8368 (t0) REVERT: F 55 GLN cc_start: 0.9114 (tt0) cc_final: 0.8765 (tt0) REVERT: F 80 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: G 11 ASP cc_start: 0.8723 (m-30) cc_final: 0.8419 (m-30) REVERT: G 117 GLU cc_start: 0.8413 (tp30) cc_final: 0.7927 (tp30) REVERT: H 90 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8712 (mtmt) REVERT: H 146 ASP cc_start: 0.8242 (t70) cc_final: 0.7875 (t0) REVERT: H 175 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8472 (tm-30) REVERT: I 2 GLU cc_start: 0.9085 (mp0) cc_final: 0.7870 (mp0) REVERT: J 27 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7809 (mp0) REVERT: J 31 ASP cc_start: 0.8511 (p0) cc_final: 0.8249 (p0) REVERT: J 52 ASP cc_start: 0.8655 (t0) cc_final: 0.8330 (t0) REVERT: J 55 GLN cc_start: 0.9143 (tt0) cc_final: 0.8825 (tt0) REVERT: J 80 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: K 11 ASP cc_start: 0.8700 (m-30) cc_final: 0.8315 (m-30) REVERT: L 146 ASP cc_start: 0.8286 (t70) cc_final: 0.7944 (t0) REVERT: L 175 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8387 (tm-30) outliers start: 30 outliers final: 11 residues processed: 269 average time/residue: 0.8295 time to fit residues: 250.8267 Evaluate side-chains 269 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 143 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 GLN L 22 HIS L 161 HIS L 247 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.055848 restraints weight = 50881.121| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.78 r_work: 0.2639 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24078 Z= 0.114 Angle : 0.528 7.670 32787 Z= 0.267 Chirality : 0.044 0.158 3765 Planarity : 0.004 0.036 4296 Dihedral : 4.205 40.389 3318 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.25 % Allowed : 11.31 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.15), residues: 3075 helix: 1.68 (0.20), residues: 771 sheet: 0.09 (0.19), residues: 705 loop : -0.34 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 23 TYR 0.009 0.001 TYR K 176 PHE 0.024 0.001 PHE H 238 TRP 0.020 0.001 TRP C 435 HIS 0.006 0.001 HIS L 161 Details of bonding type rmsd covalent geometry : bond 0.00259 (24078) covalent geometry : angle 0.52752 (32787) hydrogen bonds : bond 0.02974 ( 934) hydrogen bonds : angle 4.92368 ( 2577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 1.002 Fit side-chains REVERT: B 9 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8705 (ptmm) REVERT: B 27 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7748 (mp0) REVERT: B 31 ASP cc_start: 0.8534 (p0) cc_final: 0.8317 (p0) REVERT: B 52 ASP cc_start: 0.8592 (t0) cc_final: 0.8264 (t0) REVERT: B 55 GLN cc_start: 0.9090 (tt0) cc_final: 0.8741 (tt0) REVERT: B 78 GLU cc_start: 0.8762 (tt0) cc_final: 0.8046 (tm-30) REVERT: C 11 ASP cc_start: 0.8722 (m-30) cc_final: 0.8384 (m-30) REVERT: C 117 GLU cc_start: 0.8462 (tp30) cc_final: 0.7950 (tp30) REVERT: D 146 ASP cc_start: 0.8239 (t70) cc_final: 0.7879 (t0) REVERT: D 175 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 2 GLU cc_start: 0.9014 (mp0) cc_final: 0.7891 (mp0) REVERT: F 27 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7847 (mp0) REVERT: F 31 ASP cc_start: 0.8552 (p0) cc_final: 0.8292 (p0) REVERT: F 52 ASP cc_start: 0.8712 (t0) cc_final: 0.8280 (t0) REVERT: F 55 GLN cc_start: 0.9117 (tt0) cc_final: 0.8748 (tt0) REVERT: F 80 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: G 11 ASP cc_start: 0.8723 (m-30) cc_final: 0.8414 (m-30) REVERT: G 117 GLU cc_start: 0.8374 (tp30) cc_final: 0.7936 (tp30) REVERT: H 146 ASP cc_start: 0.8198 (t70) cc_final: 0.7385 (p0) REVERT: H 175 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8360 (tm-30) REVERT: I 2 GLU cc_start: 0.9044 (mp0) cc_final: 0.7793 (mp0) REVERT: I 58 GLU cc_start: 0.8746 (tp30) cc_final: 0.8495 (tp30) REVERT: J 27 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7823 (mp0) REVERT: J 31 ASP cc_start: 0.8475 (p0) cc_final: 0.8201 (p0) REVERT: J 52 ASP cc_start: 0.8566 (t0) cc_final: 0.8282 (t0) REVERT: J 55 GLN cc_start: 0.9122 (tt0) cc_final: 0.8790 (tt0) REVERT: J 80 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: K 11 ASP cc_start: 0.8698 (m-30) cc_final: 0.8299 (m-30) REVERT: K 117 GLU cc_start: 0.8529 (tp30) cc_final: 0.8264 (tp30) REVERT: L 146 ASP cc_start: 0.8205 (t70) cc_final: 0.7409 (p0) REVERT: L 175 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8329 (tm-30) outliers start: 31 outliers final: 8 residues processed: 285 average time/residue: 0.7768 time to fit residues: 250.4796 Evaluate side-chains 274 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 263 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 86 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN F 54 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS L 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.069996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.053842 restraints weight = 51032.783| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.77 r_work: 0.2590 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24078 Z= 0.216 Angle : 0.570 7.677 32787 Z= 0.286 Chirality : 0.045 0.162 3765 Planarity : 0.004 0.038 4296 Dihedral : 4.300 40.449 3318 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.09 % Allowed : 11.92 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.15), residues: 3075 helix: 1.82 (0.20), residues: 753 sheet: 0.04 (0.19), residues: 723 loop : -0.26 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.014 0.001 TYR K 176 PHE 0.022 0.001 PHE H 238 TRP 0.022 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00500 (24078) covalent geometry : angle 0.56951 (32787) hydrogen bonds : bond 0.03439 ( 934) hydrogen bonds : angle 5.04399 ( 2577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 1.110 Fit side-chains REVERT: B 27 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7761 (mp0) REVERT: B 31 ASP cc_start: 0.8558 (p0) cc_final: 0.8269 (p0) REVERT: B 52 ASP cc_start: 0.8649 (t0) cc_final: 0.8290 (t0) REVERT: B 55 GLN cc_start: 0.9089 (tt0) cc_final: 0.8762 (tt0) REVERT: B 78 GLU cc_start: 0.8770 (tt0) cc_final: 0.8053 (tm-30) REVERT: C 11 ASP cc_start: 0.8717 (m-30) cc_final: 0.8377 (m-30) REVERT: C 117 GLU cc_start: 0.8463 (tp30) cc_final: 0.7978 (tp30) REVERT: D 146 ASP cc_start: 0.8285 (t70) cc_final: 0.7935 (t0) REVERT: D 175 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8404 (tm-30) REVERT: F 27 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7864 (mp0) REVERT: F 31 ASP cc_start: 0.8554 (p0) cc_final: 0.8329 (p0) REVERT: F 52 ASP cc_start: 0.8736 (t0) cc_final: 0.8294 (t0) REVERT: F 55 GLN cc_start: 0.9118 (tt0) cc_final: 0.8747 (tt0) REVERT: G 11 ASP cc_start: 0.8722 (m-30) cc_final: 0.8422 (m-30) REVERT: G 117 GLU cc_start: 0.8390 (tp30) cc_final: 0.7912 (tp30) REVERT: H 146 ASP cc_start: 0.8270 (t70) cc_final: 0.7910 (t0) REVERT: H 175 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8461 (tm-30) REVERT: I 2 GLU cc_start: 0.9059 (mp0) cc_final: 0.7852 (mp0) REVERT: J 27 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7825 (mp0) REVERT: J 31 ASP cc_start: 0.8480 (p0) cc_final: 0.8226 (p0) REVERT: J 52 ASP cc_start: 0.8631 (t0) cc_final: 0.8292 (t0) REVERT: J 55 GLN cc_start: 0.9145 (tt0) cc_final: 0.8823 (tt0) REVERT: J 78 GLU cc_start: 0.8854 (tt0) cc_final: 0.8110 (tm-30) REVERT: J 80 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: K 11 ASP cc_start: 0.8707 (m-30) cc_final: 0.8323 (m-30) REVERT: K 117 GLU cc_start: 0.8518 (tp30) cc_final: 0.8236 (tp30) REVERT: L 146 ASP cc_start: 0.8320 (t70) cc_final: 0.7475 (p0) REVERT: L 175 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8406 (tm-30) outliers start: 27 outliers final: 10 residues processed: 270 average time/residue: 0.7408 time to fit residues: 226.6265 Evaluate side-chains 259 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 250 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 184 optimal weight: 0.0070 chunk 194 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 166 ASN D 247 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN H 22 HIS H 161 HIS H 247 GLN J 12 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 531 GLN L 22 HIS L 161 HIS L 247 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.052562 restraints weight = 51187.704| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.75 r_work: 0.2559 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24078 Z= 0.289 Angle : 0.620 7.998 32787 Z= 0.311 Chirality : 0.047 0.172 3765 Planarity : 0.004 0.042 4296 Dihedral : 4.488 40.941 3318 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.97 % Allowed : 12.80 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 3075 helix: 1.70 (0.20), residues: 753 sheet: -0.03 (0.18), residues: 729 loop : -0.27 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 70 TYR 0.018 0.002 TYR K 176 PHE 0.020 0.001 PHE H 238 TRP 0.022 0.001 TRP H 145 HIS 0.007 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00667 (24078) covalent geometry : angle 0.61989 (32787) hydrogen bonds : bond 0.03821 ( 934) hydrogen bonds : angle 5.17196 ( 2577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 1.000 Fit side-chains REVERT: B 27 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7764 (mp0) REVERT: B 31 ASP cc_start: 0.8558 (p0) cc_final: 0.8286 (p0) REVERT: B 52 ASP cc_start: 0.8616 (t0) cc_final: 0.8296 (t0) REVERT: B 55 GLN cc_start: 0.9062 (tt0) cc_final: 0.8742 (tt0) REVERT: B 102 GLU cc_start: 0.8131 (mp0) cc_final: 0.7922 (pm20) REVERT: C 11 ASP cc_start: 0.8728 (m-30) cc_final: 0.8369 (m-30) REVERT: C 117 GLU cc_start: 0.8469 (tp30) cc_final: 0.7927 (tp30) REVERT: D 146 ASP cc_start: 0.8375 (t70) cc_final: 0.8020 (t0) REVERT: D 175 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8474 (tm-30) REVERT: F 27 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7855 (mp0) REVERT: F 31 ASP cc_start: 0.8576 (p0) cc_final: 0.8370 (p0) REVERT: F 52 ASP cc_start: 0.8729 (t0) cc_final: 0.8310 (t0) REVERT: F 55 GLN cc_start: 0.9082 (tt0) cc_final: 0.8690 (tt0) REVERT: F 80 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8329 (mm-30) REVERT: G 11 ASP cc_start: 0.8695 (m-30) cc_final: 0.8390 (m-30) REVERT: G 117 GLU cc_start: 0.8404 (tp30) cc_final: 0.7890 (tp30) REVERT: H 146 ASP cc_start: 0.8379 (t70) cc_final: 0.8029 (t0) REVERT: H 175 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8463 (tm-30) REVERT: I 2 GLU cc_start: 0.9064 (mp0) cc_final: 0.7868 (mp0) REVERT: J 27 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7833 (mp0) REVERT: J 31 ASP cc_start: 0.8477 (p0) cc_final: 0.8225 (p0) REVERT: J 52 ASP cc_start: 0.8585 (t0) cc_final: 0.8292 (t0) REVERT: J 55 GLN cc_start: 0.9104 (tt0) cc_final: 0.8787 (tt0) REVERT: J 80 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8303 (mm-30) REVERT: K 11 ASP cc_start: 0.8690 (m-30) cc_final: 0.8299 (m-30) REVERT: K 117 GLU cc_start: 0.8526 (tp30) cc_final: 0.8263 (tp30) REVERT: L 146 ASP cc_start: 0.8388 (t70) cc_final: 0.8052 (t0) REVERT: L 175 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 24 outliers final: 6 residues processed: 262 average time/residue: 0.7820 time to fit residues: 231.8837 Evaluate side-chains 257 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 250 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 247 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 198 ASN ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 ASN L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055278 restraints weight = 50862.593| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.77 r_work: 0.2625 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24078 Z= 0.125 Angle : 0.556 9.591 32787 Z= 0.278 Chirality : 0.044 0.187 3765 Planarity : 0.004 0.037 4296 Dihedral : 4.295 40.352 3318 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.85 % Allowed : 12.96 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3075 helix: 1.81 (0.20), residues: 753 sheet: 0.27 (0.19), residues: 678 loop : -0.41 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 6 TYR 0.011 0.001 TYR H 55 PHE 0.022 0.001 PHE H 238 TRP 0.020 0.001 TRP C 435 HIS 0.006 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00286 (24078) covalent geometry : angle 0.55638 (32787) hydrogen bonds : bond 0.03053 ( 934) hydrogen bonds : angle 4.92579 ( 2577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 1.108 Fit side-chains REVERT: A 2 GLU cc_start: 0.9046 (mp0) cc_final: 0.8057 (mp0) REVERT: B 9 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8679 (ptmm) REVERT: B 27 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 31 ASP cc_start: 0.8535 (p0) cc_final: 0.8242 (p0) REVERT: B 52 ASP cc_start: 0.8605 (t0) cc_final: 0.8248 (t0) REVERT: B 55 GLN cc_start: 0.9097 (tt0) cc_final: 0.8750 (tt0) REVERT: B 78 GLU cc_start: 0.8754 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 80 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8170 (tp30) REVERT: C 11 ASP cc_start: 0.8725 (m-30) cc_final: 0.8384 (m-30) REVERT: C 117 GLU cc_start: 0.8496 (tp30) cc_final: 0.7959 (tp30) REVERT: D 146 ASP cc_start: 0.8275 (t70) cc_final: 0.7940 (t0) REVERT: D 175 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8435 (tm-30) REVERT: F 27 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7844 (mp0) REVERT: F 31 ASP cc_start: 0.8537 (p0) cc_final: 0.8310 (p0) REVERT: F 52 ASP cc_start: 0.8702 (t0) cc_final: 0.8272 (t0) REVERT: F 55 GLN cc_start: 0.9108 (tt0) cc_final: 0.8724 (tt0) REVERT: F 80 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8309 (mm-30) REVERT: G 11 ASP cc_start: 0.8725 (m-30) cc_final: 0.8416 (m-30) REVERT: G 117 GLU cc_start: 0.8385 (tp30) cc_final: 0.7934 (tp30) REVERT: H 146 ASP cc_start: 0.8253 (t70) cc_final: 0.7903 (t0) REVERT: H 175 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8425 (tm-30) REVERT: I 2 GLU cc_start: 0.9043 (mp0) cc_final: 0.7814 (mp0) REVERT: J 27 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7793 (mp0) REVERT: J 31 ASP cc_start: 0.8452 (p0) cc_final: 0.8180 (p0) REVERT: J 52 ASP cc_start: 0.8588 (t0) cc_final: 0.8262 (t0) REVERT: J 55 GLN cc_start: 0.9115 (tt0) cc_final: 0.8772 (tt0) REVERT: J 78 GLU cc_start: 0.8882 (tt0) cc_final: 0.8117 (tm-30) REVERT: J 80 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: K 11 ASP cc_start: 0.8696 (m-30) cc_final: 0.8304 (m-30) REVERT: K 60 MET cc_start: 0.9143 (pmm) cc_final: 0.8774 (pmm) REVERT: K 117 GLU cc_start: 0.8467 (tp30) cc_final: 0.8156 (tp30) REVERT: L 146 ASP cc_start: 0.8343 (t70) cc_final: 0.7494 (p0) REVERT: L 175 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 21 outliers final: 5 residues processed: 276 average time/residue: 0.7716 time to fit residues: 241.5265 Evaluate side-chains 274 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 267 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 216 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 247 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN G 251 ASN H 22 HIS H 161 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.056286 restraints weight = 50912.585| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.76 r_work: 0.2651 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24078 Z= 0.114 Angle : 0.564 10.618 32787 Z= 0.281 Chirality : 0.044 0.157 3765 Planarity : 0.004 0.038 4296 Dihedral : 4.200 40.082 3318 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.72 % Allowed : 13.53 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 3075 helix: 1.72 (0.20), residues: 774 sheet: 0.37 (0.19), residues: 642 loop : -0.41 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 6 TYR 0.010 0.001 TYR K 176 PHE 0.021 0.001 PHE H 238 TRP 0.020 0.001 TRP C 435 HIS 0.005 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00262 (24078) covalent geometry : angle 0.56448 (32787) hydrogen bonds : bond 0.02879 ( 934) hydrogen bonds : angle 4.82379 ( 2577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6150 Ramachandran restraints generated. 3075 Oldfield, 0 Emsley, 3075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 1.033 Fit side-chains REVERT: A 2 GLU cc_start: 0.9035 (mp0) cc_final: 0.8151 (mp0) REVERT: B 9 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8653 (ptmm) REVERT: B 27 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7706 (mp0) REVERT: B 31 ASP cc_start: 0.8526 (p0) cc_final: 0.8228 (p0) REVERT: B 52 ASP cc_start: 0.8556 (t0) cc_final: 0.8224 (t0) REVERT: B 55 GLN cc_start: 0.9078 (tt0) cc_final: 0.8730 (tt0) REVERT: B 78 GLU cc_start: 0.8753 (tt0) cc_final: 0.8054 (tm-30) REVERT: C 11 ASP cc_start: 0.8716 (m-30) cc_final: 0.8376 (m-30) REVERT: C 117 GLU cc_start: 0.8464 (tp30) cc_final: 0.7975 (tp30) REVERT: D 146 ASP cc_start: 0.8229 (t70) cc_final: 0.7898 (t0) REVERT: D 175 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8481 (tm-30) REVERT: F 27 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7848 (mp0) REVERT: F 31 ASP cc_start: 0.8516 (p0) cc_final: 0.8281 (p0) REVERT: F 52 ASP cc_start: 0.8714 (t0) cc_final: 0.8269 (t0) REVERT: F 55 GLN cc_start: 0.9117 (tt0) cc_final: 0.8737 (tt0) REVERT: F 80 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8283 (mm-30) REVERT: G 11 ASP cc_start: 0.8723 (m-30) cc_final: 0.8422 (m-30) REVERT: G 117 GLU cc_start: 0.8365 (tp30) cc_final: 0.7930 (tp30) REVERT: H 146 ASP cc_start: 0.8236 (t70) cc_final: 0.7427 (p0) REVERT: H 175 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8438 (tm-30) REVERT: I 2 GLU cc_start: 0.9041 (mp0) cc_final: 0.7796 (mp0) REVERT: I 65 THR cc_start: 0.8685 (p) cc_final: 0.8314 (p) REVERT: I 67 GLU cc_start: 0.8849 (pm20) cc_final: 0.8447 (pm20) REVERT: J 27 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7724 (mp0) REVERT: J 31 ASP cc_start: 0.8452 (p0) cc_final: 0.8185 (p0) REVERT: J 52 ASP cc_start: 0.8563 (t0) cc_final: 0.8252 (t0) REVERT: J 55 GLN cc_start: 0.9122 (tt0) cc_final: 0.8779 (tt0) REVERT: J 78 GLU cc_start: 0.8868 (tt0) cc_final: 0.8138 (tm-30) REVERT: J 80 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: K 11 ASP cc_start: 0.8709 (m-30) cc_final: 0.8322 (m-30) REVERT: K 60 MET cc_start: 0.9143 (pmm) cc_final: 0.8835 (pmm) REVERT: L 67 ASP cc_start: 0.8126 (m-30) cc_final: 0.7613 (m-30) REVERT: L 146 ASP cc_start: 0.8281 (t70) cc_final: 0.7481 (p0) REVERT: L 175 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8312 (tm-30) REVERT: L 189 LEU cc_start: 0.6971 (pp) cc_final: 0.6716 (pp) REVERT: L 208 ASP cc_start: 0.8774 (m-30) cc_final: 0.8238 (m-30) outliers start: 18 outliers final: 7 residues processed: 293 average time/residue: 0.7367 time to fit residues: 245.6877 Evaluate side-chains 280 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 271 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 242 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 247 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS H 161 HIS H 247 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS L 161 HIS L 247 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.053310 restraints weight = 51348.933| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.77 r_work: 0.2576 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24078 Z= 0.261 Angle : 0.626 8.674 32787 Z= 0.312 Chirality : 0.046 0.189 3765 Planarity : 0.004 0.040 4296 Dihedral : 4.413 40.634 3318 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.76 % Allowed : 14.01 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 3075 helix: 1.77 (0.20), residues: 753 sheet: 0.27 (0.19), residues: 696 loop : -0.37 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 23 TYR 0.015 0.002 TYR K 176 PHE 0.018 0.001 PHE H 238 TRP 0.020 0.001 TRP H 145 HIS 0.009 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00606 (24078) covalent geometry : angle 0.62618 (32787) hydrogen bonds : bond 0.03610 ( 934) hydrogen bonds : angle 5.05707 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7345.14 seconds wall clock time: 126 minutes 43.31 seconds (7603.31 seconds total)