Starting phenix.real_space_refine on Sat Nov 18 16:37:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/11_2023/8hcn_34659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/11_2023/8hcn_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_34659/11_2023/8hcn_34659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/11_2023/8hcn_34659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/11_2023/8hcn_34659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcn_34659/11_2023/8hcn_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 12.04, per 1000 atoms: 0.51 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: 9.17 Conformation dependent library (CDL) restraints added in 4.5 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: 8.85 Time building geometry restraints manager: 9.92 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: 1.300 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: 7.110 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 62.570 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.510 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 1.7076 time to fit residues: 663.4781 Evaluate side-chains 271 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6185 ------------------------------------------------------------------------------- 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: 0.0870 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 75 GLN C 201 GLN C 299 ASN C 349 HIS C 362 GLN C 499 ASN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN F 75 GLN G 201 GLN G 299 ASN G 349 HIS G 499 ASN H 22 HIS H 185 GLN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 75 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24078 Z= 0.236 Angle : 0.552 8.184 32787 Z= 0.281 Chirality : 0.044 0.165 3765 Planarity : 0.004 0.038 4296 Dihedral : 4.247 36.796 3318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.01 % Allowed : 7.29 % Favored : 91.71 % 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: 1.79 (0.20), residues: 759 sheet: 0.01 (0.19), residues: 708 loop : -0.37 (0.15), residues: 1608 *********************** 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 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 3.048 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 257 average time/residue: 1.5308 time to fit residues: 449.3102 Evaluate side-chains 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 2.752 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 9 average time/residue: 0.6045 time to fit residues: 10.8084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 278 optimal weight: 0.4980 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 223 optimal weight: 9.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 ** 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 K 362 GLN L 22 HIS L 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24078 Z= 0.158 Angle : 0.513 7.988 32787 Z= 0.259 Chirality : 0.043 0.159 3765 Planarity : 0.004 0.034 4296 Dihedral : 4.128 36.906 3318 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.21 % Allowed : 8.37 % Favored : 90.42 % 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: 1.87 (0.20), residues: 759 sheet: 0.11 (0.19), residues: 702 loop : -0.33 (0.16), residues: 1614 *********************** 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 322 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 292 time to evaluate : 2.835 Fit side-chains outliers start: 30 outliers final: 11 residues processed: 300 average time/residue: 1.5708 time to fit residues: 533.7151 Evaluate side-chains 272 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 10 average time/residue: 0.4333 time to fit residues: 10.1319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** C 531 GLN D 22 HIS ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** G 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1160 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= 0.295 Angle : 0.548 7.836 32787 Z= 0.277 Chirality : 0.044 0.161 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.217 37.122 3318 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.93 % Allowed : 10.67 % Favored : 88.41 % 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: 0.42 (0.15), residues: 3075 helix: 1.83 (0.20), residues: 756 sheet: 0.12 (0.19), residues: 702 loop : -0.35 (0.15), residues: 1617 *********************** 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 284 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 2.601 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 269 average time/residue: 1.5688 time to fit residues: 478.3922 Evaluate side-chains 268 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 9 average time/residue: 0.4413 time to fit residues: 9.1935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** G 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN 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 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24078 Z= 0.180 Angle : 0.516 7.537 32787 Z= 0.261 Chirality : 0.043 0.157 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.119 37.001 3318 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.85 % Allowed : 11.39 % Favored : 87.76 % 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: 0.45 (0.15), residues: 3075 helix: 1.87 (0.20), residues: 756 sheet: 0.13 (0.19), residues: 702 loop : -0.33 (0.15), residues: 1617 *********************** 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 295 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 2.823 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 284 average time/residue: 1.6050 time to fit residues: 517.5640 Evaluate side-chains 260 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 2.792 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 5 average time/residue: 0.7040 time to fit residues: 8.3147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.0370 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 245 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 G 219 HIS I 97 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24078 Z= 0.150 Angle : 0.509 7.518 32787 Z= 0.257 Chirality : 0.043 0.155 3765 Planarity : 0.004 0.052 4296 Dihedral : 4.029 37.085 3318 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 11.96 % Favored : 87.08 % 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: 1.90 (0.20), residues: 753 sheet: 0.19 (0.19), residues: 699 loop : -0.30 (0.15), residues: 1623 *********************** 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 289 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 265 time to evaluate : 2.925 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 277 average time/residue: 1.5014 time to fit residues: 475.0717 Evaluate side-chains 264 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 2.942 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 7 average time/residue: 0.9022 time to fit residues: 11.2773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 249 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 294 optimal weight: 0.8980 chunk 184 optimal weight: 0.0980 chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8670 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24078 Z= 0.147 Angle : 0.514 7.619 32787 Z= 0.258 Chirality : 0.043 0.153 3765 Planarity : 0.004 0.053 4296 Dihedral : 3.958 37.109 3318 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.97 % Allowed : 12.48 % Favored : 86.55 % 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: 756 sheet: 0.21 (0.19), residues: 699 loop : -0.26 (0.15), residues: 1620 *********************** 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 286 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 262 time to evaluate : 2.797 Fit side-chains outliers start: 24 outliers final: 7 residues processed: 275 average time/residue: 1.5020 time to fit residues: 472.9579 Evaluate side-chains 257 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 2.943 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 1.3478 time to fit residues: 8.1564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 231 optimal weight: 8.9990 chunk 268 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 ** 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: 0.8712 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24078 Z= 0.270 Angle : 0.567 9.901 32787 Z= 0.282 Chirality : 0.044 0.189 3765 Planarity : 0.004 0.051 4296 Dihedral : 4.125 37.559 3318 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.85 % Allowed : 12.80 % 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: 0.60 (0.15), residues: 3075 helix: 1.91 (0.20), residues: 753 sheet: 0.52 (0.19), residues: 660 loop : -0.33 (0.15), residues: 1662 *********************** 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 277 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 2.791 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 269 average time/residue: 1.5300 time to fit residues: 469.0023 Evaluate side-chains 266 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 5 average time/residue: 0.2755 time to fit residues: 5.9999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 274 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 273 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 J 55 GLN K 7 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: 0.8730 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24078 Z= 0.343 Angle : 0.593 10.442 32787 Z= 0.297 Chirality : 0.045 0.160 3765 Planarity : 0.004 0.050 4296 Dihedral : 4.297 38.307 3318 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.64 % Allowed : 13.77 % Favored : 85.59 % 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: 1.82 (0.20), residues: 753 sheet: 0.49 (0.19), residues: 660 loop : -0.37 (0.15), residues: 1662 *********************** 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 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 259 time to evaluate : 2.770 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 267 average time/residue: 1.6068 time to fit residues: 490.1898 Evaluate side-chains 257 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 249 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 3 average time/residue: 0.9185 time to fit residues: 7.0347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 304 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** E 81 GLN F 55 GLN I 97 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24078 Z= 0.190 Angle : 0.562 9.120 32787 Z= 0.282 Chirality : 0.044 0.161 3765 Planarity : 0.004 0.052 4296 Dihedral : 4.182 38.142 3318 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.48 % Allowed : 14.05 % Favored : 85.47 % 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: 1.84 (0.20), residues: 753 sheet: 0.52 (0.20), residues: 660 loop : -0.36 (0.15), residues: 1662 ********************** 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 275 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 2.822 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 272 average time/residue: 1.5645 time to fit residues: 484.3255 Evaluate side-chains 268 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.2645 time to fit residues: 3.9753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 0.0970 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN ** 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 = 0.3129 r_free = 0.3129 target = 0.072105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.056191 restraints weight = 50986.219| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.74 r_work: 0.2644 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24078 Z= 0.220 Angle : 0.562 8.687 32787 Z= 0.282 Chirality : 0.044 0.174 3765 Planarity : 0.004 0.052 4296 Dihedral : 4.173 37.941 3318 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.44 % Allowed : 14.29 % Favored : 85.27 % 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: 1.84 (0.20), residues: 753 sheet: 0.53 (0.20), residues: 660 loop : -0.36 (0.15), residues: 1662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7904.10 seconds wall clock time: 142 minutes 9.44 seconds (8529.44 seconds total)