Starting phenix.real_space_refine on Mon Feb 19 03:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_34659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_34659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_34659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_34659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/02_2024/8hcn_34659.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 12.30, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.41 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 2.95 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: 8.81 Time building geometry restraints manager: 10.07 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: 99.35 - 106.33: 879 106.33 - 113.30: 13356 113.30 - 120.28: 8168 120.28 - 127.25: 10040 127.25 - 134.23: 344 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 2.440 nonbonded pdb=" OG SER G 297 " pdb=" OE2 GLU G 345 " model vdw 2.212 2.440 nonbonded pdb=" O LEU C 566 " pdb=" NH1 ARG E 23 " model vdw 2.215 2.520 nonbonded pdb=" O LEU G 566 " pdb=" NH1 ARG I 23 " model vdw 2.222 2.520 nonbonded pdb=" O PRO B 64 " pdb=" OG1 THR B 67 " model vdw 2.231 2.440 ... (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 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.990 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 62.440 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.920 ------------------------------------------------------------------------------- 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= 0.198 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (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 TRP 0.047 0.002 TRP D 145 HIS 0.004 0.001 HIS G 415 PHE 0.007 0.001 PHE H 238 TYR 0.007 0.001 TYR D 204 ARG 0.002 0.000 ARG C 338 *********************** 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 fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.874 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: 1.6701 time to fit residues: 648.8292 Evaluate side-chains 255 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 277 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN C 7 GLN C 201 GLN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN C 349 HIS C 362 GLN C 499 ASN C 531 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN G 7 GLN G 201 GLN G 299 ASN G 349 HIS G 499 ASN H 22 HIS H 185 GLN J 55 GLN J 75 GLN K 7 GLN K 201 GLN ** K 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 HIS K 499 ASN K 521 GLN L 22 HIS L 161 HIS L 185 GLN ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24078 Z= 0.247 Angle : 0.548 8.226 32787 Z= 0.277 Chirality : 0.044 0.166 3765 Planarity : 0.004 0.038 4296 Dihedral : 4.263 36.723 3318 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.09 % Allowed : 6.88 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3075 helix: 1.83 (0.20), residues: 756 sheet: -0.07 (0.19), residues: 696 loop : -0.35 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 145 HIS 0.004 0.001 HIS G 472 PHE 0.007 0.001 PHE K 565 TYR 0.011 0.001 TYR H 55 ARG 0.003 0.000 ARG B 23 *********************** 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 284 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 257 time to evaluate : 2.676 Fit side-chains REVERT: B 9 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8801 (ptmm) REVERT: B 27 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7729 (mp0) REVERT: B 31 ASP cc_start: 0.8198 (p0) cc_final: 0.7873 (p0) REVERT: B 52 ASP cc_start: 0.8666 (t0) cc_final: 0.8355 (t0) REVERT: B 55 GLN cc_start: 0.8635 (tt0) cc_final: 0.8403 (tt0) REVERT: B 78 GLU cc_start: 0.8421 (tt0) cc_final: 0.8050 (tm-30) REVERT: C 11 ASP cc_start: 0.8336 (m-30) cc_final: 0.8038 (m-30) REVERT: C 334 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7132 (tp30) REVERT: D 146 ASP cc_start: 0.8130 (t70) cc_final: 0.7732 (t0) REVERT: D 175 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8384 (tm-30) REVERT: E 2 GLU cc_start: 0.8756 (mp0) cc_final: 0.7710 (mp0) REVERT: F 27 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7810 (mp0) REVERT: F 31 ASP cc_start: 0.8273 (p0) cc_final: 0.7938 (p0) REVERT: F 52 ASP cc_start: 0.8673 (t0) cc_final: 0.8456 (t0) REVERT: F 55 GLN cc_start: 0.8667 (tt0) cc_final: 0.8352 (tt0) REVERT: G 11 ASP cc_start: 0.8345 (m-30) cc_final: 0.8084 (m-30) REVERT: H 146 ASP cc_start: 0.8083 (t70) cc_final: 0.7411 (p0) REVERT: H 175 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8336 (tm-30) REVERT: I 65 THR cc_start: 0.8843 (p) cc_final: 0.8577 (p) REVERT: I 67 GLU cc_start: 0.8194 (pm20) cc_final: 0.7941 (pm20) REVERT: J 27 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7750 (mp0) REVERT: J 31 ASP cc_start: 0.8211 (p0) cc_final: 0.7861 (p0) REVERT: J 52 ASP cc_start: 0.8658 (t0) cc_final: 0.8436 (t0) REVERT: J 55 GLN cc_start: 0.8880 (tt0) cc_final: 0.8627 (tt0) REVERT: J 80 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: K 11 ASP cc_start: 0.8348 (m-30) cc_final: 0.8055 (m-30) REVERT: L 146 ASP cc_start: 0.8081 (t70) cc_final: 0.7410 (p0) REVERT: L 175 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8166 (tm-30) outliers start: 27 outliers final: 10 residues processed: 266 average time/residue: 1.4956 time to fit residues: 452.0321 Evaluate side-chains 266 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 254 time to evaluate : 2.910 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain H residue 22 HIS Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 246 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 278 optimal weight: 0.5980 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 GLN L 22 HIS L 161 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24078 Z= 0.234 Angle : 0.527 7.947 32787 Z= 0.266 Chirality : 0.044 0.162 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.211 37.236 3318 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.25 % Allowed : 8.09 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3075 helix: 1.86 (0.20), residues: 756 sheet: 0.08 (0.19), residues: 702 loop : -0.36 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 145 HIS 0.009 0.001 HIS H 22 PHE 0.012 0.001 PHE H 21 TYR 0.009 0.001 TYR D 204 ARG 0.002 0.000 ARG A 6 *********************** 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 299 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.995 Fit side-chains REVERT: B 5 GLU cc_start: 0.8797 (pt0) cc_final: 0.8333 (pt0) REVERT: B 9 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: B 27 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7726 (mp0) REVERT: B 31 ASP cc_start: 0.8197 (p0) cc_final: 0.7874 (p0) REVERT: B 52 ASP cc_start: 0.8702 (t0) cc_final: 0.8345 (t0) REVERT: B 55 GLN cc_start: 0.8580 (tt0) cc_final: 0.8316 (tt0) REVERT: C 11 ASP cc_start: 0.8392 (m-30) cc_final: 0.8132 (m-30) REVERT: C 334 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7161 (tp30) REVERT: C 508 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8075 (mmm160) REVERT: D 146 ASP cc_start: 0.8121 (t70) cc_final: 0.7749 (t0) REVERT: D 175 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 2 GLU cc_start: 0.8778 (mp0) cc_final: 0.7744 (mp0) REVERT: F 27 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7817 (mp0) REVERT: F 31 ASP cc_start: 0.8266 (p0) cc_final: 0.7970 (p0) REVERT: F 52 ASP cc_start: 0.8697 (t0) cc_final: 0.8429 (t0) REVERT: F 55 GLN cc_start: 0.8680 (tt0) cc_final: 0.8360 (tt0) REVERT: F 80 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: G 11 ASP cc_start: 0.8420 (m-30) cc_final: 0.8167 (m-30) REVERT: H 146 ASP cc_start: 0.8068 (t70) cc_final: 0.7415 (p0) REVERT: H 175 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8349 (tm-30) REVERT: I 2 GLU cc_start: 0.8910 (mp0) cc_final: 0.7701 (mp0) REVERT: I 65 THR cc_start: 0.8838 (p) cc_final: 0.8566 (p) REVERT: I 67 GLU cc_start: 0.8196 (pm20) cc_final: 0.7941 (pm20) REVERT: J 27 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7815 (mp0) REVERT: J 31 ASP cc_start: 0.8211 (p0) cc_final: 0.7862 (p0) REVERT: J 52 ASP cc_start: 0.8672 (t0) cc_final: 0.8427 (t0) REVERT: J 55 GLN cc_start: 0.8841 (tt0) cc_final: 0.8622 (tt0) REVERT: J 80 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: K 11 ASP cc_start: 0.8392 (m-30) cc_final: 0.8089 (m-30) REVERT: L 146 ASP cc_start: 0.8076 (t70) cc_final: 0.7396 (p0) REVERT: L 175 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8255 (tm-30) outliers start: 31 outliers final: 12 residues processed: 278 average time/residue: 1.5303 time to fit residues: 481.5695 Evaluate side-chains 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 259 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 271 ILE 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 H residue 246 CYS Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 246 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 279 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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** F 55 GLN H 22 HIS J 55 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 299 ASN L 22 HIS ** L 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24078 Z= 0.206 Angle : 0.513 7.753 32787 Z= 0.259 Chirality : 0.043 0.159 3765 Planarity : 0.004 0.053 4296 Dihedral : 4.145 37.196 3318 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.13 % Allowed : 9.46 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3075 helix: 1.89 (0.20), residues: 756 sheet: 0.10 (0.19), residues: 702 loop : -0.35 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 PHE 0.007 0.001 PHE G 565 TYR 0.009 0.001 TYR D 204 ARG 0.002 0.000 ARG J 23 *********************** 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 300 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 272 time to evaluate : 2.658 Fit side-chains REVERT: B 5 GLU cc_start: 0.8799 (pt0) cc_final: 0.8327 (pt0) REVERT: B 9 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8836 (ptmm) REVERT: B 27 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7781 (mp0) REVERT: B 31 ASP cc_start: 0.8192 (p0) cc_final: 0.7866 (p0) REVERT: B 52 ASP cc_start: 0.8634 (t0) cc_final: 0.8379 (t0) REVERT: B 55 GLN cc_start: 0.8637 (tt0) cc_final: 0.8282 (tt0) REVERT: C 11 ASP cc_start: 0.8380 (m-30) cc_final: 0.8118 (m-30) REVERT: C 334 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7171 (tp30) REVERT: D 146 ASP cc_start: 0.8102 (t70) cc_final: 0.7747 (t0) REVERT: D 175 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8422 (tm-30) REVERT: E 2 GLU cc_start: 0.8778 (mp0) cc_final: 0.7741 (mp0) REVERT: F 27 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7823 (mp0) REVERT: F 31 ASP cc_start: 0.8262 (p0) cc_final: 0.7966 (p0) REVERT: F 52 ASP cc_start: 0.8687 (t0) cc_final: 0.8354 (t0) REVERT: F 55 GLN cc_start: 0.8659 (tt0) cc_final: 0.8375 (tt0) REVERT: F 80 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: G 11 ASP cc_start: 0.8406 (m-30) cc_final: 0.8151 (m-30) REVERT: G 117 GLU cc_start: 0.7854 (tp30) cc_final: 0.7649 (tp30) REVERT: H 146 ASP cc_start: 0.8059 (t70) cc_final: 0.7414 (p0) REVERT: H 175 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8347 (tm-30) REVERT: I 2 GLU cc_start: 0.8899 (mp0) cc_final: 0.7706 (mp0) REVERT: I 65 THR cc_start: 0.8817 (p) cc_final: 0.8578 (p) REVERT: I 67 GLU cc_start: 0.8199 (pm20) cc_final: 0.7953 (pm20) REVERT: J 27 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7823 (mp0) REVERT: J 31 ASP cc_start: 0.8207 (p0) cc_final: 0.7859 (p0) REVERT: J 52 ASP cc_start: 0.8626 (t0) cc_final: 0.8402 (t0) REVERT: J 55 GLN cc_start: 0.8882 (tt0) cc_final: 0.8649 (tt0) REVERT: J 76 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8616 (ttpp) REVERT: J 80 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: K 11 ASP cc_start: 0.8389 (m-30) cc_final: 0.8081 (m-30) REVERT: L 146 ASP cc_start: 0.8082 (t70) cc_final: 0.7440 (p0) REVERT: L 175 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8251 (tm-30) outliers start: 28 outliers final: 11 residues processed: 277 average time/residue: 1.5695 time to fit residues: 491.8613 Evaluate side-chains 272 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 271 ILE 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 H residue 246 CYS Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 271 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 HIS J 55 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24078 Z= 0.420 Angle : 0.587 8.052 32787 Z= 0.295 Chirality : 0.046 0.167 3765 Planarity : 0.004 0.052 4296 Dihedral : 4.386 37.677 3318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.25 % Allowed : 10.75 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3075 helix: 1.73 (0.20), residues: 756 sheet: 0.33 (0.19), residues: 699 loop : -0.40 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 145 HIS 0.006 0.001 HIS C 134 PHE 0.025 0.001 PHE H 238 TYR 0.014 0.001 TYR D 204 ARG 0.003 0.000 ARG J 23 *********************** 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 290 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 2.736 Fit side-chains REVERT: B 9 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8827 (ptmm) REVERT: B 27 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7792 (mp0) REVERT: B 31 ASP cc_start: 0.8227 (p0) cc_final: 0.7903 (p0) REVERT: B 52 ASP cc_start: 0.8698 (t0) cc_final: 0.8409 (t0) REVERT: B 55 GLN cc_start: 0.8605 (tt0) cc_final: 0.8280 (tt0) REVERT: B 76 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8476 (ttpp) REVERT: C 11 ASP cc_start: 0.8393 (m-30) cc_final: 0.8088 (m-30) REVERT: D 146 ASP cc_start: 0.8171 (t70) cc_final: 0.7823 (t0) REVERT: D 175 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8435 (tm-30) REVERT: E 2 GLU cc_start: 0.8824 (mp0) cc_final: 0.7778 (mp0) REVERT: F 27 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7837 (mp0) REVERT: F 31 ASP cc_start: 0.8272 (p0) cc_final: 0.7995 (p0) REVERT: F 52 ASP cc_start: 0.8754 (t0) cc_final: 0.8413 (t0) REVERT: F 55 GLN cc_start: 0.8869 (tt0) cc_final: 0.8606 (tt0) REVERT: F 77 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7964 (tpp80) REVERT: F 80 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: G 11 ASP cc_start: 0.8415 (m-30) cc_final: 0.8167 (m-30) REVERT: G 117 GLU cc_start: 0.7909 (tp30) cc_final: 0.7645 (tp30) REVERT: H 146 ASP cc_start: 0.8082 (t70) cc_final: 0.7739 (t0) REVERT: H 175 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8416 (tm-30) REVERT: I 2 GLU cc_start: 0.8911 (mp0) cc_final: 0.7713 (mp0) REVERT: J 27 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7828 (mp0) REVERT: J 31 ASP cc_start: 0.8222 (p0) cc_final: 0.7910 (p0) REVERT: J 52 ASP cc_start: 0.8671 (t0) cc_final: 0.8420 (t0) REVERT: J 55 GLN cc_start: 0.8843 (tt0) cc_final: 0.8615 (tt0) REVERT: J 80 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: K 11 ASP cc_start: 0.8377 (m-30) cc_final: 0.8071 (m-30) REVERT: L 146 ASP cc_start: 0.8212 (t70) cc_final: 0.7901 (t0) REVERT: L 175 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 31 outliers final: 12 residues processed: 268 average time/residue: 1.5915 time to fit residues: 482.3920 Evaluate side-chains 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 259 time to evaluate : 2.674 ------------------------------------------------------------------------------- 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 119 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain F residue 77 ARG 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 K residue 315 MET 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 99 optimal weight: 10.0000 chunk 266 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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** H 22 HIS I 97 ASN J 55 GLN ** K 134 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24078 Z= 0.222 Angle : 0.529 7.793 32787 Z= 0.267 Chirality : 0.044 0.160 3765 Planarity : 0.004 0.053 4296 Dihedral : 4.238 37.641 3318 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.25 % Allowed : 11.51 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3075 helix: 1.79 (0.20), residues: 753 sheet: 0.35 (0.19), residues: 663 loop : -0.41 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 PHE 0.022 0.001 PHE H 238 TYR 0.010 0.001 TYR D 204 ARG 0.002 0.000 ARG J 23 *********************** 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 302 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 271 time to evaluate : 2.691 Fit side-chains REVERT: A 2 GLU cc_start: 0.8807 (mp0) cc_final: 0.7842 (mp0) REVERT: B 5 GLU cc_start: 0.8732 (pt0) cc_final: 0.8343 (pt0) REVERT: B 9 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8835 (ptmm) REVERT: B 23 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8051 (mtp85) REVERT: B 27 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 31 ASP cc_start: 0.8199 (p0) cc_final: 0.7879 (p0) REVERT: B 52 ASP cc_start: 0.8647 (t0) cc_final: 0.8381 (t0) REVERT: B 55 GLN cc_start: 0.8614 (tt0) cc_final: 0.8259 (tt0) REVERT: B 78 GLU cc_start: 0.8407 (tt0) cc_final: 0.7918 (tm-30) REVERT: C 11 ASP cc_start: 0.8376 (m-30) cc_final: 0.8111 (m-30) REVERT: C 117 GLU cc_start: 0.7968 (tp30) cc_final: 0.7767 (tp30) REVERT: D 146 ASP cc_start: 0.8138 (t70) cc_final: 0.7801 (t0) REVERT: D 175 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8373 (tm-30) REVERT: E 2 GLU cc_start: 0.8773 (mp0) cc_final: 0.7705 (mp0) REVERT: F 27 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7825 (mp0) REVERT: F 31 ASP cc_start: 0.8261 (p0) cc_final: 0.7977 (p0) REVERT: F 52 ASP cc_start: 0.8725 (t0) cc_final: 0.8372 (t0) REVERT: F 55 GLN cc_start: 0.8861 (tt0) cc_final: 0.8588 (tt0) REVERT: F 72 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: F 80 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: G 11 ASP cc_start: 0.8397 (m-30) cc_final: 0.8140 (m-30) REVERT: G 117 GLU cc_start: 0.7864 (tp30) cc_final: 0.7597 (tp30) REVERT: H 146 ASP cc_start: 0.8058 (t70) cc_final: 0.7727 (t0) REVERT: H 175 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8344 (tm-30) REVERT: I 2 GLU cc_start: 0.8884 (mp0) cc_final: 0.7645 (mp0) REVERT: J 9 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8798 (ptmm) REVERT: J 27 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7729 (mp0) REVERT: J 31 ASP cc_start: 0.8208 (p0) cc_final: 0.7872 (p0) REVERT: J 52 ASP cc_start: 0.8610 (t0) cc_final: 0.8381 (t0) REVERT: J 55 GLN cc_start: 0.8864 (tt0) cc_final: 0.8590 (tt0) REVERT: J 80 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: K 11 ASP cc_start: 0.8390 (m-30) cc_final: 0.8059 (m-30) REVERT: L 146 ASP cc_start: 0.8202 (t70) cc_final: 0.7484 (p0) REVERT: L 175 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8359 (tm-30) outliers start: 31 outliers final: 11 residues processed: 280 average time/residue: 1.6310 time to fit residues: 516.3122 Evaluate side-chains 269 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 27 LYS Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain J residue 9 LYS 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 285 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 0.0570 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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** H 22 HIS I 97 ASN J 55 GLN ** K 134 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24078 Z= 0.167 Angle : 0.513 8.109 32787 Z= 0.258 Chirality : 0.043 0.155 3765 Planarity : 0.004 0.053 4296 Dihedral : 4.098 37.550 3318 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.25 % Allowed : 11.71 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3075 helix: 1.88 (0.20), residues: 753 sheet: 0.44 (0.19), residues: 660 loop : -0.40 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS L 161 PHE 0.021 0.001 PHE H 238 TYR 0.007 0.001 TYR D 204 ARG 0.002 0.000 ARG J 23 *********************** 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 301 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 2.954 Fit side-chains REVERT: A 2 GLU cc_start: 0.8792 (mp0) cc_final: 0.7817 (mp0) REVERT: A 58 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8071 (tp30) REVERT: B 5 GLU cc_start: 0.8750 (pt0) cc_final: 0.8437 (pt0) REVERT: B 9 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8814 (ptmm) REVERT: B 23 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8142 (mtp85) REVERT: B 27 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7783 (mp0) REVERT: B 31 ASP cc_start: 0.8189 (p0) cc_final: 0.7927 (p0) REVERT: B 52 ASP cc_start: 0.8635 (t0) cc_final: 0.8350 (t0) REVERT: B 55 GLN cc_start: 0.8618 (tt0) cc_final: 0.8286 (tt0) REVERT: B 78 GLU cc_start: 0.8404 (tt0) cc_final: 0.7973 (tm-30) REVERT: C 11 ASP cc_start: 0.8372 (m-30) cc_final: 0.8123 (m-30) REVERT: D 146 ASP cc_start: 0.8145 (t70) cc_final: 0.7829 (t0) REVERT: D 175 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8346 (tm-30) REVERT: F 27 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7829 (mp0) REVERT: F 31 ASP cc_start: 0.8249 (p0) cc_final: 0.7954 (p0) REVERT: F 52 ASP cc_start: 0.8686 (t0) cc_final: 0.8336 (t0) REVERT: F 55 GLN cc_start: 0.8846 (tt0) cc_final: 0.8574 (tt0) REVERT: F 72 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: F 80 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7887 (mm-30) REVERT: G 11 ASP cc_start: 0.8390 (m-30) cc_final: 0.8130 (m-30) REVERT: G 117 GLU cc_start: 0.7843 (tp30) cc_final: 0.7599 (tp30) REVERT: H 146 ASP cc_start: 0.8057 (t70) cc_final: 0.7421 (p0) REVERT: H 175 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8372 (tm-30) REVERT: I 2 GLU cc_start: 0.8855 (mp0) cc_final: 0.7632 (mp0) REVERT: J 9 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8783 (ptmm) REVERT: J 27 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7732 (mp0) REVERT: J 31 ASP cc_start: 0.8198 (p0) cc_final: 0.7852 (p0) REVERT: J 52 ASP cc_start: 0.8661 (t0) cc_final: 0.8397 (t0) REVERT: J 55 GLN cc_start: 0.8857 (tt0) cc_final: 0.8613 (tt0) REVERT: J 76 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8576 (ttpp) REVERT: J 78 GLU cc_start: 0.8410 (tt0) cc_final: 0.7941 (tm-30) REVERT: J 80 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: K 11 ASP cc_start: 0.8393 (m-30) cc_final: 0.8070 (m-30) REVERT: L 146 ASP cc_start: 0.8146 (t70) cc_final: 0.7477 (p0) REVERT: L 175 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8314 (tm-30) outliers start: 31 outliers final: 7 residues processed: 284 average time/residue: 1.4510 time to fit residues: 469.8175 Evaluate side-chains 268 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 257 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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 27 LYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain J residue 9 LYS 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 182 optimal weight: 7.9990 chunk 117 optimal weight: 0.0570 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 6.9990 chunk 268 optimal weight: 0.5980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** 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** H 22 HIS I 97 ASN J 55 GLN ** K 134 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24078 Z= 0.153 Angle : 0.528 10.895 32787 Z= 0.261 Chirality : 0.043 0.202 3765 Planarity : 0.004 0.053 4296 Dihedral : 4.027 37.436 3318 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.81 % Allowed : 12.68 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3075 helix: 1.93 (0.20), residues: 753 sheet: 0.48 (0.19), residues: 660 loop : -0.38 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS L 161 PHE 0.020 0.001 PHE H 238 TYR 0.008 0.001 TYR K 176 ARG 0.002 0.000 ARG D 232 *********************** 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 289 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 269 time to evaluate : 2.671 Fit side-chains REVERT: A 2 GLU cc_start: 0.8775 (mp0) cc_final: 0.7807 (mp0) REVERT: A 58 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8111 (tp30) REVERT: B 5 GLU cc_start: 0.8726 (pt0) cc_final: 0.8395 (pt0) REVERT: B 9 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8787 (ptmm) REVERT: B 23 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8169 (mtp85) REVERT: B 27 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7799 (mp0) REVERT: B 31 ASP cc_start: 0.8186 (p0) cc_final: 0.7923 (p0) REVERT: B 52 ASP cc_start: 0.8559 (t0) cc_final: 0.8281 (t0) REVERT: B 55 GLN cc_start: 0.8620 (tt0) cc_final: 0.8245 (tt0) REVERT: B 78 GLU cc_start: 0.8402 (tt0) cc_final: 0.7974 (tm-30) REVERT: C 11 ASP cc_start: 0.8363 (m-30) cc_final: 0.8114 (m-30) REVERT: D 146 ASP cc_start: 0.8130 (t70) cc_final: 0.7814 (t0) REVERT: D 175 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8437 (tm-30) REVERT: F 27 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7839 (mp0) REVERT: F 31 ASP cc_start: 0.8229 (p0) cc_final: 0.7932 (p0) REVERT: F 52 ASP cc_start: 0.8664 (t0) cc_final: 0.8290 (t0) REVERT: F 55 GLN cc_start: 0.8833 (tt0) cc_final: 0.8537 (tt0) REVERT: F 72 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: F 80 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7854 (mm-30) REVERT: G 11 ASP cc_start: 0.8380 (m-30) cc_final: 0.8113 (m-30) REVERT: G 144 GLU cc_start: 0.7948 (tt0) cc_final: 0.7746 (tp30) REVERT: H 146 ASP cc_start: 0.8050 (t70) cc_final: 0.7429 (p0) REVERT: H 175 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8376 (tm-30) REVERT: I 2 GLU cc_start: 0.8863 (mp0) cc_final: 0.7658 (mp0) REVERT: I 65 THR cc_start: 0.8826 (p) cc_final: 0.8596 (p) REVERT: I 67 GLU cc_start: 0.8180 (pm20) cc_final: 0.7915 (pm20) REVERT: J 9 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8771 (ptmm) REVERT: J 27 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7740 (mp0) REVERT: J 31 ASP cc_start: 0.8194 (p0) cc_final: 0.7832 (p0) REVERT: J 52 ASP cc_start: 0.8577 (t0) cc_final: 0.8345 (t0) REVERT: J 55 GLN cc_start: 0.8877 (tt0) cc_final: 0.8638 (tt0) REVERT: J 76 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8612 (ttpp) REVERT: J 80 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: K 11 ASP cc_start: 0.8393 (m-30) cc_final: 0.8082 (m-30) REVERT: L 146 ASP cc_start: 0.8128 (t70) cc_final: 0.7486 (p0) REVERT: L 175 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8299 (tm-30) outliers start: 20 outliers final: 4 residues processed: 279 average time/residue: 1.4728 time to fit residues: 467.7915 Evaluate side-chains 268 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 260 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain C residue 435 TRP Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain J residue 9 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS H 22 HIS J 55 GLN ** K 134 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24078 Z= 0.350 Angle : 0.569 8.292 32787 Z= 0.284 Chirality : 0.045 0.168 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.211 37.899 3318 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.89 % Allowed : 12.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3075 helix: 1.86 (0.20), residues: 753 sheet: 0.44 (0.19), residues: 666 loop : -0.38 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS C 134 PHE 0.019 0.001 PHE H 238 TYR 0.016 0.001 TYR K 176 ARG 0.005 0.000 ARG J 23 *********************** 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 273 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 2.622 Fit side-chains REVERT: A 2 GLU cc_start: 0.8840 (mp0) cc_final: 0.7867 (mp0) REVERT: A 58 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8120 (tp30) REVERT: B 5 GLU cc_start: 0.8742 (pt0) cc_final: 0.8364 (pt0) REVERT: B 27 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7795 (mp0) REVERT: B 31 ASP cc_start: 0.8214 (p0) cc_final: 0.7881 (p0) REVERT: B 52 ASP cc_start: 0.8625 (t0) cc_final: 0.8044 (t70) REVERT: B 55 GLN cc_start: 0.8643 (tt0) cc_final: 0.8106 (tt0) REVERT: B 80 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7799 (tp30) REVERT: C 11 ASP cc_start: 0.8375 (m-30) cc_final: 0.8112 (m-30) REVERT: D 146 ASP cc_start: 0.8219 (t70) cc_final: 0.7909 (t0) REVERT: D 175 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8458 (tm-30) REVERT: F 27 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7839 (mp0) REVERT: F 31 ASP cc_start: 0.8265 (p0) cc_final: 0.7991 (p0) REVERT: F 52 ASP cc_start: 0.8732 (t0) cc_final: 0.8374 (t0) REVERT: F 55 GLN cc_start: 0.8857 (tt0) cc_final: 0.8557 (tt0) REVERT: F 72 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: F 80 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7850 (mm-30) REVERT: G 11 ASP cc_start: 0.8392 (m-30) cc_final: 0.8136 (m-30) REVERT: H 146 ASP cc_start: 0.8135 (t70) cc_final: 0.7801 (t0) REVERT: H 175 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8456 (tm-30) REVERT: I 2 GLU cc_start: 0.8890 (mp0) cc_final: 0.7661 (mp0) REVERT: I 34 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8311 (mt-10) REVERT: J 9 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8790 (ptmm) REVERT: J 27 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7765 (mp0) REVERT: J 31 ASP cc_start: 0.8223 (p0) cc_final: 0.7879 (p0) REVERT: J 52 ASP cc_start: 0.8655 (t0) cc_final: 0.8382 (t0) REVERT: J 55 GLN cc_start: 0.8874 (tt0) cc_final: 0.8644 (tt0) REVERT: J 76 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8658 (ttpp) REVERT: J 78 GLU cc_start: 0.8454 (tt0) cc_final: 0.7865 (tm-30) REVERT: J 80 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: K 11 ASP cc_start: 0.8383 (m-30) cc_final: 0.8062 (m-30) REVERT: L 146 ASP cc_start: 0.8206 (t70) cc_final: 0.7488 (p0) REVERT: L 175 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 22 outliers final: 8 residues processed: 260 average time/residue: 1.5203 time to fit residues: 451.1750 Evaluate side-chains 256 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 9 LYS Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain J residue 9 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 290 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 242 optimal weight: 0.0470 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS H 22 HIS J 55 GLN ** K 134 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24078 Z= 0.276 Angle : 0.564 10.333 32787 Z= 0.280 Chirality : 0.044 0.158 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.222 38.165 3318 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.60 % Allowed : 13.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3075 helix: 1.81 (0.20), residues: 756 sheet: 0.43 (0.19), residues: 666 loop : -0.37 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.005 0.001 HIS K 134 PHE 0.019 0.001 PHE H 238 TYR 0.013 0.001 TYR K 176 ARG 0.004 0.000 ARG J 23 ********************** 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 267 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 252 time to evaluate : 2.949 Fit side-chains REVERT: A 2 GLU cc_start: 0.8827 (mp0) cc_final: 0.7844 (mp0) REVERT: A 58 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8106 (tp30) REVERT: B 5 GLU cc_start: 0.8733 (pt0) cc_final: 0.8350 (pt0) REVERT: B 27 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7790 (mp0) REVERT: B 31 ASP cc_start: 0.8198 (p0) cc_final: 0.7879 (p0) REVERT: B 52 ASP cc_start: 0.8579 (t0) cc_final: 0.7983 (t70) REVERT: B 55 GLN cc_start: 0.8646 (tt0) cc_final: 0.8076 (tt0) REVERT: B 80 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7914 (tp30) REVERT: C 11 ASP cc_start: 0.8376 (m-30) cc_final: 0.8113 (m-30) REVERT: C 117 GLU cc_start: 0.7993 (tp30) cc_final: 0.7769 (tp30) REVERT: D 146 ASP cc_start: 0.8229 (t70) cc_final: 0.7932 (t0) REVERT: D 175 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8436 (tm-30) REVERT: F 27 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7838 (mp0) REVERT: F 31 ASP cc_start: 0.8263 (p0) cc_final: 0.7984 (p0) REVERT: F 52 ASP cc_start: 0.8703 (t0) cc_final: 0.8346 (t0) REVERT: F 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8528 (tt0) REVERT: F 72 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: F 80 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7863 (mm-30) REVERT: G 11 ASP cc_start: 0.8394 (m-30) cc_final: 0.8134 (m-30) REVERT: H 146 ASP cc_start: 0.8142 (t70) cc_final: 0.7812 (t0) REVERT: H 175 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8404 (tm-30) REVERT: I 2 GLU cc_start: 0.8871 (mp0) cc_final: 0.7671 (mp0) REVERT: J 9 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8789 (ptmm) REVERT: J 27 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7801 (mp0) REVERT: J 31 ASP cc_start: 0.8217 (p0) cc_final: 0.7871 (p0) REVERT: J 52 ASP cc_start: 0.8585 (t0) cc_final: 0.8351 (t0) REVERT: J 55 GLN cc_start: 0.8879 (tt0) cc_final: 0.8614 (tt0) REVERT: J 76 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8639 (ttpp) REVERT: J 78 GLU cc_start: 0.8453 (tt0) cc_final: 0.7863 (tm-30) REVERT: J 80 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: K 11 ASP cc_start: 0.8390 (m-30) cc_final: 0.8067 (m-30) REVERT: L 146 ASP cc_start: 0.8202 (t70) cc_final: 0.7487 (p0) REVERT: L 175 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 15 outliers final: 8 residues processed: 258 average time/residue: 1.5543 time to fit residues: 454.7317 Evaluate side-chains 260 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 249 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 246 CYS Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain J residue 9 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 258 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 223 optimal weight: 0.0870 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 44 optimal weight: 0.1980 chunk 213 optimal weight: 4.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS H 22 HIS ** K 134 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.056193 restraints weight = 50910.733| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.77 r_work: 0.2643 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1362 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= 0.168 Angle : 0.533 8.675 32787 Z= 0.265 Chirality : 0.043 0.154 3765 Planarity : 0.004 0.052 4296 Dihedral : 4.105 37.875 3318 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.60 % Allowed : 13.37 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3075 helix: 1.88 (0.20), residues: 756 sheet: 0.48 (0.19), residues: 666 loop : -0.35 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 145 HIS 0.011 0.001 HIS G 134 PHE 0.020 0.001 PHE H 238 TYR 0.010 0.001 TYR K 176 ARG 0.006 0.000 ARG J 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7822.12 seconds wall clock time: 140 minutes 31.61 seconds (8431.61 seconds total)