Starting phenix.real_space_refine on Wed Nov 20 06:44:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/11_2024/7tfj_25874.cif" } resolution = 3.3 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= 0.042 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 370 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: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 56 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 12880 2.51 5 N 3516 2.21 5 O 4052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3130 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2685 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.61, per 1000 atoms: 0.66 Number of scatterers: 20607 At special positions: 0 Unit cell: (119.232, 122.544, 137.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 18 33.99 S 81 16.00 P 56 15.00 Mg 4 11.99 O 4052 8.00 N 3516 7.00 C 12880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 2.8 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 15 sheets defined 50.7% alpha, 14.9% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 6.70 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.521A pdb=" N TYR A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.751A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.572A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.280A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.521A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.508A pdb=" N PHE A 466 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.505A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.369A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.363A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.689A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.186A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.502A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.617A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 668 through 691 removed outlier: 3.663A pdb=" N ARG A 691 " --> pdb=" O HIS A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.538A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.515A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.725A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.880A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.603A pdb=" N TYR C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.572A pdb=" N MET C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.090A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.991A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.562A pdb=" N CYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.544A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.868A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.606A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.077A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.898A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.548A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.551A pdb=" N GLU D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 39' Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.914A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.339A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.773A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.141A pdb=" N LYS E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.409A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 105 through 119 removed outlier: 3.543A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.016A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.660A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.674A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.976A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 221 Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.122A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.713A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'H' and resid 9 through 19 Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.748A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 215 Processing helix chain 'H' and resid 216 through 221 removed outlier: 4.337A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 352 removed outlier: 8.061A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.923A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.093A pdb=" N LEU B 76 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 114 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 78 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.573A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.924A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.808A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.081A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.511A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 62 removed outlier: 4.350A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 116 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR H 163 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MSE H 161 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.124A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.986A pdb=" N VAL F 203 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 102 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.741A pdb=" N VAL G 26 " --> pdb=" O MSE G 70 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR G 136 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 157 through 158 Processing sheet with id=AB5, first strand: chain 'G' and resid 167 through 172 removed outlier: 3.715A pdb=" N ILE G 167 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER G 177 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR H 114 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.546A pdb=" N VAL H 66 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 26 " --> pdb=" O MSE H 70 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 29 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6811 1.37 - 1.52: 8059 1.52 - 1.67: 5998 1.67 - 1.82: 115 1.82 - 1.97: 40 Bond restraints: 21023 Sorted by residual: bond pdb=" N GLU B 287 " pdb=" CA GLU B 287 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.94e+00 bond pdb=" CG GLU C 307 " pdb=" CD GLU C 307 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" N GLN E 110 " pdb=" CA GLN E 110 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.20e+00 bond pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.49e-02 4.50e+03 3.69e+00 bond pdb=" C LYS A 550 " pdb=" N PRO A 551 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 3.01e+00 ... (remaining 21018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28093 2.07 - 4.14: 419 4.14 - 6.22: 76 6.22 - 8.29: 10 8.29 - 10.36: 3 Bond angle restraints: 28601 Sorted by residual: angle pdb=" N GLU C 307 " pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " ideal model delta sigma weight residual 110.28 118.10 -7.82 1.55e+00 4.16e-01 2.54e+01 angle pdb=" CA ARG E 106 " pdb=" CB ARG E 106 " pdb=" CG ARG E 106 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.23 3.73 1.00e+00 1.00e+00 1.39e+01 angle pdb=" C GLU A 293 " pdb=" N GLU A 294 " pdb=" CA GLU A 294 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 ... (remaining 28596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 12302 30.79 - 61.58: 497 61.58 - 92.37: 22 92.37 - 123.17: 1 123.17 - 153.96: 2 Dihedral angle restraints: 12824 sinusoidal: 5560 harmonic: 7264 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.91 118.91 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 86.23 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C4' DT J 19 " pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " pdb=" P DA J 20 " ideal model delta sinusoidal sigma weight residual 220.00 85.93 134.07 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 12821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2314 0.037 - 0.075: 759 0.075 - 0.112: 204 0.112 - 0.150: 48 0.150 - 0.187: 5 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASP D 178 " pdb=" N ASP D 178 " pdb=" C ASP D 178 " pdb=" CB ASP D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PHE H 19 " pdb=" N PHE H 19 " pdb=" C PHE H 19 " pdb=" CB PHE H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB THR H 193 " pdb=" CA THR H 193 " pdb=" OG1 THR H 193 " pdb=" CG2 THR H 193 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3327 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 251 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO H 252 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO H 252 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO H 252 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.061 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO E 63 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 680 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TYR A 680 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 680 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 681 " 0.014 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 302 2.65 - 3.21: 18898 3.21 - 3.78: 31952 3.78 - 4.34: 43913 4.34 - 4.90: 72576 Nonbonded interactions: 167641 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.088 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.142 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.151 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.164 2.170 ... (remaining 167636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } 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: 4.320 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 52.970 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.079 21023 Z= 0.205 Angle : 0.627 10.361 28601 Z= 0.333 Chirality : 0.041 0.187 3330 Planarity : 0.005 0.132 3483 Dihedral : 15.192 153.957 8096 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.17), residues: 2466 helix: 1.09 (0.16), residues: 1127 sheet: -0.35 (0.25), residues: 469 loop : -0.77 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 543 HIS 0.004 0.001 HIS B 232 PHE 0.028 0.001 PHE A 335 TYR 0.016 0.001 TYR A 596 ARG 0.011 0.000 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 2.545 Fit side-chains revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7704 (pm20) cc_final: 0.6718 (tt0) REVERT: A 399 MET cc_start: 0.7742 (ppp) cc_final: 0.7037 (ppp) REVERT: A 414 LEU cc_start: 0.7176 (mm) cc_final: 0.6861 (mm) REVERT: A 660 MET cc_start: 0.7036 (mtm) cc_final: 0.6800 (ttm) REVERT: A 666 PHE cc_start: 0.6949 (t80) cc_final: 0.6279 (t80) REVERT: D 115 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.7303 (ttp-170) REVERT: E 258 ASP cc_start: 0.7952 (p0) cc_final: 0.7742 (p0) REVERT: G 149 ARG cc_start: 0.8370 (mtm110) cc_final: 0.8056 (mtm180) REVERT: G 228 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7847 (mtt90) REVERT: H 215 ILE cc_start: 0.7806 (pt) cc_final: 0.7526 (pt) REVERT: H 238 GLN cc_start: 0.7922 (tt0) cc_final: 0.6981 (tm-30) outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.3470 time to fit residues: 193.9911 Evaluate side-chains 284 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS B 146 GLN C 184 HIS D 124 HIS ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21023 Z= 0.221 Angle : 0.577 11.880 28601 Z= 0.301 Chirality : 0.041 0.150 3330 Planarity : 0.004 0.081 3483 Dihedral : 14.146 134.873 3208 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.04 % Allowed : 8.30 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2466 helix: 1.36 (0.16), residues: 1145 sheet: -0.21 (0.26), residues: 447 loop : -0.63 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 323 HIS 0.010 0.001 HIS E 93 PHE 0.017 0.001 PHE H 19 TYR 0.020 0.001 TYR B 186 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 GLU cc_start: 0.7714 (pm20) cc_final: 0.6839 (tt0) REVERT: A 399 MET cc_start: 0.7610 (ppp) cc_final: 0.5576 (mtt) REVERT: A 632 ARG cc_start: 0.7770 (mtt-85) cc_final: 0.7204 (mtt-85) REVERT: A 666 PHE cc_start: 0.7147 (t80) cc_final: 0.6421 (t80) REVERT: B 129 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7308 (tpp-160) REVERT: C 140 ASN cc_start: 0.7695 (p0) cc_final: 0.7472 (p0) REVERT: C 307 GLU cc_start: 0.6521 (mp0) cc_final: 0.6263 (mp0) REVERT: D 282 GLU cc_start: 0.7287 (tt0) cc_final: 0.7070 (tt0) REVERT: E 95 GLU cc_start: 0.7700 (mp0) cc_final: 0.7430 (mp0) REVERT: G 149 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8099 (mtm110) REVERT: G 223 ASP cc_start: 0.6011 (p0) cc_final: 0.5627 (p0) REVERT: H 14 ARG cc_start: 0.8850 (mtm-85) cc_final: 0.8186 (mtm180) REVERT: H 61 ARG cc_start: 0.6794 (ttm170) cc_final: 0.6072 (ptt90) REVERT: H 238 GLN cc_start: 0.7995 (tt0) cc_final: 0.6956 (tm-30) outliers start: 23 outliers final: 18 residues processed: 332 average time/residue: 0.3743 time to fit residues: 184.2039 Evaluate side-chains 303 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 175 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 225 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 HIS G 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.005 0.049 21023 Z= 0.310 Angle : 0.581 9.719 28601 Z= 0.302 Chirality : 0.041 0.152 3330 Planarity : 0.004 0.062 3483 Dihedral : 14.266 135.390 3205 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.86 % Allowed : 10.88 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2466 helix: 1.37 (0.16), residues: 1147 sheet: -0.35 (0.24), residues: 484 loop : -0.54 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 323 HIS 0.018 0.001 HIS D 124 PHE 0.024 0.002 PHE A 335 TYR 0.023 0.002 TYR B 186 ARG 0.006 0.001 ARG G 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.7578 (ppp) cc_final: 0.5630 (mtt) REVERT: B 129 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7060 (tpp-160) REVERT: B 133 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7429 (mp) REVERT: C 17 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: C 140 ASN cc_start: 0.7745 (p0) cc_final: 0.7543 (p0) REVERT: C 307 GLU cc_start: 0.6500 (mp0) cc_final: 0.6253 (mp0) REVERT: D 282 GLU cc_start: 0.7284 (tt0) cc_final: 0.7053 (tt0) REVERT: G 149 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8149 (mtm110) REVERT: G 223 ASP cc_start: 0.5950 (p0) cc_final: 0.5591 (p0) REVERT: H 14 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8177 (mtm-85) REVERT: H 61 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6115 (ptt90) REVERT: H 238 GLN cc_start: 0.8018 (tt0) cc_final: 0.7108 (tm-30) outliers start: 41 outliers final: 31 residues processed: 320 average time/residue: 0.3725 time to fit residues: 177.2867 Evaluate side-chains 311 residues out of total 2207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 595 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 119 MSE Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-dev-5513/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-dev-5513/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-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-dev-5513/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-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-dev-5513/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-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3844 > 50: distance: 58 - 72: 3.020 distance: 91 - 95: 27.044 distance: 95 - 96: 18.424 distance: 96 - 97: 41.687 distance: 96 - 99: 48.849 distance: 97 - 98: 33.747 distance: 97 - 107: 38.395 distance: 99 - 100: 38.757 distance: 100 - 101: 42.030 distance: 100 - 102: 7.631 distance: 101 - 103: 16.246 distance: 102 - 104: 28.442 distance: 103 - 105: 21.459 distance: 104 - 105: 39.169 distance: 105 - 106: 24.093 distance: 107 - 108: 53.862 distance: 108 - 109: 39.389 distance: 108 - 111: 26.166 distance: 109 - 110: 25.031 distance: 109 - 114: 31.599 distance: 111 - 112: 35.591 distance: 111 - 113: 19.135 distance: 114 - 115: 19.509 distance: 115 - 116: 23.375 distance: 115 - 118: 38.087 distance: 116 - 117: 44.474 distance: 116 - 121: 10.969 distance: 118 - 119: 43.305 distance: 118 - 120: 27.408 distance: 121 - 122: 16.212 distance: 122 - 123: 18.469 distance: 122 - 125: 26.869 distance: 123 - 124: 32.499 distance: 123 - 132: 19.590 distance: 125 - 126: 13.982 distance: 126 - 127: 23.218 distance: 127 - 128: 17.140 distance: 128 - 129: 13.739 distance: 129 - 130: 17.004 distance: 129 - 131: 31.625 distance: 132 - 133: 38.205 distance: 133 - 134: 30.842 distance: 133 - 136: 46.924 distance: 134 - 135: 24.732 distance: 134 - 140: 37.562 distance: 136 - 137: 11.610 distance: 136 - 138: 25.391 distance: 137 - 139: 12.652 distance: 140 - 141: 50.576 distance: 141 - 142: 42.748 distance: 141 - 144: 31.960 distance: 142 - 143: 12.625 distance: 142 - 148: 6.782 distance: 143 - 171: 45.236 distance: 144 - 145: 32.062 distance: 144 - 146: 23.549 distance: 145 - 147: 39.545 distance: 148 - 149: 46.383 distance: 149 - 150: 44.642 distance: 149 - 152: 29.810 distance: 150 - 151: 39.975 distance: 150 - 156: 26.231 distance: 151 - 176: 14.994 distance: 152 - 153: 28.894 distance: 153 - 154: 43.646 distance: 153 - 155: 28.011 distance: 156 - 157: 25.279 distance: 156 - 162: 24.370 distance: 157 - 158: 38.136 distance: 157 - 160: 9.068 distance: 158 - 159: 35.972 distance: 158 - 163: 6.511 distance: 159 - 182: 22.355 distance: 160 - 161: 19.328 distance: 161 - 162: 27.184 distance: 163 - 164: 31.954 distance: 164 - 165: 26.775 distance: 164 - 167: 31.783 distance: 165 - 166: 21.546 distance: 165 - 171: 40.328 distance: 166 - 191: 22.129 distance: 167 - 168: 26.059 distance: 168 - 169: 7.253 distance: 168 - 170: 8.471 distance: 171 - 172: 21.637 distance: 172 - 173: 12.581 distance: 172 - 175: 12.254 distance: 173 - 174: 20.239 distance: 173 - 176: 9.377