Starting phenix.real_space_refine on Mon Dec 11 23:27:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jau_36134/12_2023/8jau_36134.pdb" } resolution = 3.22 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 93 5.16 5 C 10893 2.51 5 N 2918 2.21 5 O 3159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17064 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "I" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2382 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 401 SG CYS A 54 49.333 59.267 98.815 1.00 24.05 S ATOM 8881 SG CYS B 54 45.488 59.582 98.089 1.00 35.11 S Time building chain proxies: 9.10, per 1000 atoms: 0.53 Number of scatterers: 17064 At special positions: 0 Unit cell: (107.42, 135.3, 202.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 93 16.00 O 3159 8.00 N 2918 7.00 C 10893 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: 6.81 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 5 sheets defined 75.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.786A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.782A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.729A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.906A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.242A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.620A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.954A pdb=" N GLU A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.404A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 4.013A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.532A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.102A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.785A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.756A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.610A pdb=" N HIS A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.532A pdb=" N GLU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 3.624A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 528 removed outlier: 3.736A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.578A pdb=" N VAL A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 4.104A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.630A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.553A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 152 removed outlier: 4.038A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.582A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.716A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.616A pdb=" N PHE E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 230 removed outlier: 3.596A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 3.507A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP E 245 " --> pdb=" O GLY E 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 254 " --> pdb=" O CYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 264 removed outlier: 3.731A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 271 Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.547A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 3.537A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.973A pdb=" N GLY D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 84 removed outlier: 4.338A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.638A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.796A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.897A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.569A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 72 No H-bonds generated for 'chain 'B' and resid 71 through 72' Processing helix chain 'B' and resid 73 through 74 No H-bonds generated for 'chain 'B' and resid 73 through 74' Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.552A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 removed outlier: 3.730A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.252A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.810A pdb=" N TRP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 198 removed outlier: 3.772A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 241 through 259 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.908A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.648A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 368 removed outlier: 4.319A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.231A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 463 removed outlier: 4.033A pdb=" N GLN B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 489 through 506 Processing helix chain 'B' and resid 507 through 510 removed outlier: 3.731A pdb=" N TYR B 510 " --> pdb=" O GLY B 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 511 through 528 removed outlier: 4.104A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 Processing helix chain 'B' and resid 569 through 577 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.532A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.619A pdb=" N GLN G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'H' and resid 33 through 37 Processing helix chain 'H' and resid 39 through 46 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.185A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.676A pdb=" N LEU H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.605A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.752A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 78 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.517A pdb=" N MET I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 4.034A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.693A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 3.781A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 195 removed outlier: 4.315A pdb=" N TYR I 194 " --> pdb=" O VAL I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 205 Processing helix chain 'I' and resid 207 through 228 removed outlier: 4.186A pdb=" N GLN I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 254 removed outlier: 3.630A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 271 removed outlier: 3.571A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 289 removed outlier: 3.523A pdb=" N LEU I 278 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE I 286 " --> pdb=" O CYS I 282 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I 287 " --> pdb=" O HIS I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 298 removed outlier: 5.144A pdb=" N ASN I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR I 298 " --> pdb=" O MET I 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.819A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG C 8 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU C 44 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 51 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 removed outlier: 8.068A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.520A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 75 " --> pdb=" O MET G 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 32 removed outlier: 7.868A pdb=" N VAL H 60 " --> pdb=" O TYR H 18 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS H 20 " --> pdb=" O VAL H 60 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3186 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: 4.97 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5569 1.34 - 1.46: 3486 1.46 - 1.58: 8237 1.58 - 1.69: 0 1.69 - 1.81: 139 Bond restraints: 17431 Sorted by residual: bond pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" N MET I 26 " pdb=" CA MET I 26 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CB VAL B 246 " pdb=" CG1 VAL B 246 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB THR A 290 " pdb=" CG2 THR A 290 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" CB THR B 290 " pdb=" CG2 THR B 290 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 ... (remaining 17426 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 333 106.31 - 113.23: 9433 113.23 - 120.16: 6385 120.16 - 127.08: 7203 127.08 - 134.01: 163 Bond angle restraints: 23517 Sorted by residual: angle pdb=" C GLU H 54 " pdb=" N ASN H 55 " pdb=" CA ASN H 55 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL H 69 " pdb=" CA VAL H 69 " pdb=" C VAL H 69 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N GLY B 324 " pdb=" CA GLY B 324 " pdb=" C GLY B 324 " ideal model delta sigma weight residual 110.21 113.05 -2.84 9.10e-01 1.21e+00 9.74e+00 angle pdb=" C SER B 552 " pdb=" N VAL B 553 " pdb=" CA VAL B 553 " ideal model delta sigma weight residual 121.97 127.48 -5.51 1.80e+00 3.09e-01 9.36e+00 angle pdb=" C GLU E 80 " pdb=" N GLU E 81 " pdb=" CA GLU E 81 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.95e+00 ... (remaining 23512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9447 17.93 - 35.85: 869 35.85 - 53.78: 138 53.78 - 71.71: 30 71.71 - 89.63: 23 Dihedral angle restraints: 10507 sinusoidal: 4304 harmonic: 6203 Sorted by residual: dihedral pdb=" CA HIS A 221 " pdb=" C HIS A 221 " pdb=" N TYR A 222 " pdb=" CA TYR A 222 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N ILE B 304 " pdb=" CA ILE B 304 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " pdb=" CG ASP G 48 " pdb=" OD1 ASP G 48 " ideal model delta sinusoidal sigma weight residual -30.00 -89.95 59.95 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1925 0.043 - 0.086: 552 0.086 - 0.129: 76 0.129 - 0.172: 4 0.172 - 0.215: 1 Chirality restraints: 2558 Sorted by residual: chirality pdb=" CB ILE G 14 " pdb=" CA ILE G 14 " pdb=" CG1 ILE G 14 " pdb=" CG2 ILE G 14 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASN H 55 " pdb=" N ASN H 55 " pdb=" C ASN H 55 " pdb=" CB ASN H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA GLU B 568 " pdb=" N GLU B 568 " pdb=" C GLU B 568 " pdb=" CB GLU B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 2555 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS I 255 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO I 256 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 256 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 256 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 37 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 38 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 49 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO I 50 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " -0.022 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 744 2.73 - 3.27: 17917 3.27 - 3.81: 29430 3.81 - 4.36: 35752 4.36 - 4.90: 61436 Nonbonded interactions: 145279 Sorted by model distance: nonbonded pdb=" OH TYR I 219 " pdb=" OE1 GLU I 246 " model vdw 2.183 2.440 nonbonded pdb=" OG1 THR C 23 " pdb=" OE1 GLU C 26 " model vdw 2.245 2.440 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN B 434 " model vdw 2.282 2.520 nonbonded pdb=" ND2 ASN B 482 " pdb=" O GLY B 519 " model vdw 2.282 2.520 nonbonded pdb=" NH1 ARG B 103 " pdb=" OH TYR B 107 " model vdw 2.289 2.520 ... (remaining 145274 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 'B' and resid 8 through 578) } ncs_group { reference = (chain 'C' and resid 2 through 97) selection = (chain 'G' and resid 2 through 97) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 280) } ncs_group { reference = chain 'F' selection = chain 'S' } 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 28.020 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 48.710 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.004 0.041 17431 Z= 0.255 Angle : 0.520 6.830 23517 Z= 0.281 Chirality : 0.038 0.215 2558 Planarity : 0.004 0.057 3009 Dihedral : 14.397 89.633 6503 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.99 (0.17), residues: 2072 helix: -0.10 (0.13), residues: 1456 sheet: -1.44 (1.14), residues: 21 loop : -1.79 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.009 0.001 HIS B 410 PHE 0.029 0.002 PHE C 79 TYR 0.020 0.001 TYR A 294 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.205 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3339 time to fit residues: 135.5561 Evaluate side-chains 191 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.0020 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 119 optimal weight: 0.0980 chunk 186 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 333 HIS A 352 ASN E 36 ASN E 193 GLN E 225 ASN E 274 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 1 GLN B 38 ASN B 153 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN I 82 GLN I 116 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17431 Z= 0.176 Angle : 0.480 5.718 23517 Z= 0.263 Chirality : 0.036 0.153 2558 Planarity : 0.004 0.052 3009 Dihedral : 4.047 19.453 2310 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.49 % Allowed : 5.46 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.12 (0.18), residues: 2072 helix: 0.56 (0.13), residues: 1502 sheet: -1.56 (1.06), residues: 21 loop : -1.65 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 279 PHE 0.024 0.001 PHE A 445 TYR 0.017 0.001 TYR E 253 ARG 0.005 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 2.019 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 214 average time/residue: 0.3030 time to fit residues: 99.5073 Evaluate side-chains 197 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1659 time to fit residues: 4.5360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN D 108 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.004 0.029 17431 Z= 0.243 Angle : 0.475 5.781 23517 Z= 0.256 Chirality : 0.037 0.166 2558 Planarity : 0.004 0.052 3009 Dihedral : 4.015 19.194 2310 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.81 % Allowed : 8.11 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.07 (0.18), residues: 2072 helix: 0.72 (0.13), residues: 1497 sheet: -2.14 (0.74), residues: 40 loop : -1.56 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 35 HIS 0.003 0.001 HIS A 452 PHE 0.014 0.001 PHE E 64 TYR 0.023 0.001 TYR E 253 ARG 0.004 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 2.071 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 209 average time/residue: 0.2956 time to fit residues: 95.2805 Evaluate side-chains 194 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1515 time to fit residues: 5.3450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 HIS G 49 GLN H 108 ASN ** I 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17431 Z= 0.253 Angle : 0.473 5.156 23517 Z= 0.255 Chirality : 0.037 0.178 2558 Planarity : 0.003 0.052 3009 Dihedral : 4.020 19.301 2310 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.87 % Allowed : 10.28 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.15 (0.18), residues: 2072 helix: 0.78 (0.13), residues: 1501 sheet: -2.22 (0.73), residues: 40 loop : -1.54 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 35 HIS 0.003 0.001 HIS A 410 PHE 0.013 0.001 PHE B 101 TYR 0.017 0.001 TYR A 294 ARG 0.006 0.000 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.040 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 205 average time/residue: 0.3065 time to fit residues: 95.3250 Evaluate side-chains 193 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1624 time to fit residues: 6.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8904 > 50: distance: 78 - 170: 8.376 distance: 81 - 167: 24.220 distance: 120 - 125: 16.243 distance: 125 - 126: 7.125 distance: 126 - 127: 6.064 distance: 127 - 128: 4.567 distance: 127 - 129: 4.906 distance: 129 - 130: 14.837 distance: 130 - 131: 8.489 distance: 130 - 133: 15.313 distance: 131 - 132: 26.936 distance: 133 - 134: 17.237 distance: 134 - 135: 13.842 distance: 134 - 136: 22.019 distance: 135 - 137: 23.872 distance: 136 - 138: 25.774 distance: 137 - 138: 33.831 distance: 140 - 141: 34.777 distance: 140 - 143: 19.786 distance: 141 - 142: 26.260 distance: 141 - 148: 28.706 distance: 143 - 144: 47.563 distance: 144 - 145: 15.349 distance: 145 - 146: 27.187 distance: 145 - 147: 17.531 distance: 148 - 149: 21.242 distance: 149 - 150: 17.024 distance: 149 - 152: 32.936 distance: 150 - 151: 8.292 distance: 150 - 159: 17.660 distance: 152 - 153: 23.380 distance: 153 - 154: 33.794 distance: 153 - 155: 18.763 distance: 154 - 156: 26.301 distance: 155 - 157: 11.360 distance: 156 - 158: 31.100 distance: 157 - 158: 13.197 distance: 159 - 160: 17.734 distance: 160 - 161: 12.824 distance: 160 - 163: 16.480 distance: 161 - 162: 23.874 distance: 161 - 167: 4.230 distance: 163 - 164: 41.840 distance: 163 - 165: 9.376 distance: 164 - 166: 34.803 distance: 167 - 168: 16.816 distance: 168 - 169: 14.894 distance: 168 - 171: 18.401 distance: 169 - 170: 13.954 distance: 169 - 174: 10.798 distance: 171 - 172: 29.468 distance: 171 - 173: 11.003 distance: 174 - 175: 19.399 distance: 175 - 176: 49.606 distance: 175 - 178: 42.489 distance: 176 - 177: 30.134 distance: 176 - 183: 48.881 distance: 178 - 179: 50.140 distance: 179 - 180: 34.863 distance: 180 - 181: 44.356 distance: 181 - 182: 15.190 distance: 183 - 184: 30.622 distance: 184 - 185: 35.160 distance: 184 - 187: 32.763 distance: 185 - 186: 6.606 distance: 185 - 194: 30.441 distance: 186 - 218: 30.602 distance: 187 - 188: 25.388 distance: 188 - 189: 39.619 distance: 189 - 190: 38.895 distance: 190 - 191: 24.674 distance: 191 - 192: 8.727 distance: 191 - 193: 9.383 distance: 194 - 195: 20.962 distance: 195 - 196: 16.877 distance: 195 - 198: 10.771 distance: 196 - 197: 35.798 distance: 196 - 203: 18.054 distance: 198 - 199: 26.470 distance: 199 - 200: 3.440 distance: 200 - 201: 10.195 distance: 200 - 202: 24.085 distance: 203 - 204: 28.000 distance: 204 - 205: 29.882 distance: 204 - 207: 6.288 distance: 205 - 206: 26.783 distance: 205 - 213: 5.622 distance: 207 - 208: 27.956 distance: 208 - 209: 43.298 distance: 208 - 210: 36.526 distance: 210 - 212: 36.458 distance: 211 - 212: 35.068 distance: 255 - 267: 3.013