Starting phenix.real_space_refine on Thu Mar 5 09:15:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfi_25873/03_2026/7tfi_25873.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 12861 2.51 5 N 3507 2.21 5 O 4046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20573 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3097 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 2 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: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2694 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} 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: 4.64, per 1000 atoms: 0.23 Number of scatterers: 20573 At special positions: 0 Unit cell: (120.06, 123.372, 144.9, 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 4046 8.00 N 3507 7.00 C 12861 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: 1.65 Conformation dependent library (CDL) restraints added in 722.9 milliseconds 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 18 sheets defined 50.6% alpha, 13.9% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.016A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.685A pdb=" N LEU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.691A pdb=" N ASP A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 407 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 460 through 469 Proline residue: A 465 - end of helix removed outlier: 4.469A pdb=" N ARG A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 469 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 4.064A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.027A pdb=" N ILE A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.259A 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 Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.543A pdb=" N SER A 569 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.731A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.686A pdb=" N CYS A 620 " --> pdb=" O GLU A 616 " (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 654 removed outlier: 5.592A pdb=" N TYR A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 668 through 691 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.854A pdb=" N SER B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 4.086A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 116 through 119 removed outlier: 3.567A pdb=" N MET B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.542A pdb=" N GLN B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.611A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.523A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.575A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.831A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.845A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.062A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 255 through 270 removed outlier: 4.327A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.913A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 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: 4.077A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.563A 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: 4.450A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 removed outlier: 3.957A pdb=" N LEU D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.689A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.678A pdb=" N GLY D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.550A pdb=" N GLN D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.219A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 removed outlier: 3.583A pdb=" N LEU E 36 " --> pdb=" O PRO E 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 36' Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.219A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.052A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.526A 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: 3.560A 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 309 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.139A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 23 removed outlier: 4.125A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.583A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.172A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 222 removed outlier: 3.754A pdb=" N SER F 222 " --> pdb=" O SER F 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 219 through 222' Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.140A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.552A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.985A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.982A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'H' and resid 10 through 20 Processing helix chain 'H' and resid 72 through 82 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 163 through 166 Processing helix chain 'H' and resid 209 through 217 removed outlier: 4.262A pdb=" N ASP H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 221 removed outlier: 3.510A pdb=" N LEU H 221 " --> pdb=" O GLY H 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 221' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.217A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.142A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.705A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.422A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.048A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 42 removed outlier: 5.964A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.715A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG E 166 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 2 through 4 removed outlier: 3.654A pdb=" N ARG F 61 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.869A pdb=" N VAL F 26 " --> pdb=" O MSE F 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MSE F 70 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.605A pdb=" N VAL F 48 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN F 247 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 250 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.914A pdb=" N ILE F 91 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE F 100 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 207 removed outlier: 3.772A pdb=" N LYS F 168 " --> pdb=" O MSE F 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 104 " --> pdb=" O THR G 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR G 87 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.224A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 49 " --> pdb=" O GLN G 247 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 177 through 178 Processing sheet with id=AB6, first strand: chain 'G' and resid 177 through 178 removed outlier: 4.566A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.693A pdb=" N PHE H 103 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.632A pdb=" N VAL H 26 " --> pdb=" O MSE H 70 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 180 through 181 removed outlier: 3.830A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) 998 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6749 1.36 - 1.51: 5570 1.51 - 1.66: 8514 1.66 - 1.80: 91 1.80 - 1.95: 64 Bond restraints: 20988 Sorted by residual: bond pdb=" CB TRP C 256 " pdb=" CG TRP C 256 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.95e+00 bond pdb=" C TYR E 161 " pdb=" N SER E 162 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.54e+00 bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" CG1 ILE H 215 " pdb=" CD1 ILE H 215 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" C4 ADP E 500 " pdb=" C5 ADP E 500 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 20983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 27768 1.53 - 3.06: 625 3.06 - 4.59: 107 4.59 - 6.12: 45 6.12 - 7.65: 9 Bond angle restraints: 28554 Sorted by residual: angle pdb=" C ILE C 275 " pdb=" N ASP C 276 " pdb=" CA ASP C 276 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" N VAL A 469 " pdb=" CA VAL A 469 " pdb=" C VAL A 469 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" N MSE G 70 " pdb=" CA MSE G 70 " pdb=" C MSE G 70 " ideal model delta sigma weight residual 108.86 113.98 -5.12 1.41e+00 5.03e-01 1.32e+01 angle pdb=" N MSE G 199 " pdb=" CA MSE G 199 " pdb=" C MSE G 199 " ideal model delta sigma weight residual 108.26 113.81 -5.55 1.66e+00 3.63e-01 1.12e+01 angle pdb=" CA LYS G 164 " pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 ... (remaining 28549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 12046 26.67 - 53.33: 696 53.33 - 80.00: 52 80.00 - 106.66: 7 106.66 - 133.33: 3 Dihedral angle restraints: 12804 sinusoidal: 5555 harmonic: 7249 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 -173.80 113.79 1 2.00e+01 2.50e-03 3.37e+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 65.60 -133.33 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA THR A 599 " pdb=" C THR A 599 " pdb=" N ARG A 600 " pdb=" CA ARG A 600 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2362 0.039 - 0.078: 726 0.078 - 0.118: 210 0.118 - 0.157: 27 0.157 - 0.196: 1 Chirality restraints: 3326 Sorted by residual: chirality pdb=" CA GLU E 111 " pdb=" N GLU E 111 " pdb=" C GLU E 111 " pdb=" CB GLU E 111 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA GLU C 279 " pdb=" N GLU C 279 " pdb=" C GLU C 279 " pdb=" CB GLU C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-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 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 3323 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 276 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ASP C 276 " 0.067 2.00e-02 2.50e+03 pdb=" O ASP C 276 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 277 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 183 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO H 184 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 184 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 184 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 327 " 0.015 2.00e-02 2.50e+03 1.38e-02 4.73e+00 pdb=" CG TRP A 327 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 327 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 327 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 327 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 327 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 327 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 327 " 0.002 2.00e-02 2.50e+03 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 208 2.62 - 3.19: 17968 3.19 - 3.76: 31987 3.76 - 4.33: 43723 4.33 - 4.90: 72463 Nonbonded interactions: 166349 Sorted by model distance: nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.049 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.061 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.093 2.170 nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.105 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.111 2.170 ... (remaining 166344 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.043 20988 Z= 0.131 Angle : 0.601 7.647 28554 Z= 0.313 Chirality : 0.041 0.196 3326 Planarity : 0.004 0.055 3476 Dihedral : 15.251 133.330 8084 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2458 helix: 0.94 (0.16), residues: 1145 sheet: -0.88 (0.24), residues: 490 loop : -0.74 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 69 TYR 0.011 0.001 TYR A 404 PHE 0.021 0.001 PHE H 19 TRP 0.037 0.002 TRP A 327 HIS 0.009 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00285 (20988) covalent geometry : angle 0.60134 (28554) hydrogen bonds : bond 0.18060 ( 1029) hydrogen bonds : angle 7.42693 ( 2937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7729 (tpt) cc_final: 0.7396 (tpt) REVERT: A 322 ASN cc_start: 0.7955 (m-40) cc_final: 0.7506 (m-40) REVERT: C 99 ASP cc_start: 0.7170 (m-30) cc_final: 0.6922 (m-30) REVERT: D 134 TYR cc_start: 0.8798 (p90) cc_final: 0.8469 (p90) REVERT: E 58 GLU cc_start: 0.6986 (pt0) cc_final: 0.6769 (pt0) REVERT: E 107 ILE cc_start: 0.8845 (pt) cc_final: 0.8620 (pt) REVERT: E 119 MET cc_start: 0.6824 (mmm) cc_final: 0.6498 (mmm) REVERT: E 292 HIS cc_start: 0.7763 (t70) cc_final: 0.7006 (t-90) REVERT: E 323 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 199 MSE cc_start: 0.5232 (mtt) cc_final: 0.1580 (tpt) REVERT: G 30 CYS cc_start: 0.7857 (m) cc_final: 0.7516 (t) REVERT: G 80 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7975 (mmm160) REVERT: H 159 ASN cc_start: 0.8468 (p0) cc_final: 0.8191 (p0) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.1373 time to fit residues: 79.0318 Evaluate side-chains 262 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 321 GLN E 74 GLN E 104 ASN E 224 GLN E 227 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114422 restraints weight = 30363.472| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.56 r_work: 0.3345 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20988 Z= 0.137 Angle : 0.581 7.375 28554 Z= 0.304 Chirality : 0.041 0.186 3326 Planarity : 0.004 0.049 3476 Dihedral : 13.676 133.320 3198 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.23 % Allowed : 8.44 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2458 helix: 1.30 (0.16), residues: 1146 sheet: -0.82 (0.23), residues: 497 loop : -0.57 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 600 TYR 0.017 0.001 TYR B 186 PHE 0.026 0.001 PHE F 245 TRP 0.016 0.002 TRP A 327 HIS 0.009 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00301 (20988) covalent geometry : angle 0.58093 (28554) hydrogen bonds : bond 0.04930 ( 1029) hydrogen bonds : angle 5.34552 ( 2937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.792 Fit side-chains REVERT: A 318 MET cc_start: 0.7989 (tpt) cc_final: 0.7428 (tpt) REVERT: A 322 ASN cc_start: 0.8070 (m-40) cc_final: 0.7592 (m-40) REVERT: A 467 ASP cc_start: 0.7629 (p0) cc_final: 0.7426 (p0) REVERT: A 636 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7619 (tp40) REVERT: C 99 ASP cc_start: 0.7773 (m-30) cc_final: 0.7527 (m-30) REVERT: D 31 TYR cc_start: 0.8823 (m-80) cc_final: 0.8584 (m-80) REVERT: E 119 MET cc_start: 0.6412 (mmm) cc_final: 0.6071 (mmm) REVERT: F 199 MSE cc_start: 0.5533 (mtt) cc_final: 0.1672 (tpt) outliers start: 27 outliers final: 17 residues processed: 309 average time/residue: 0.1420 time to fit residues: 68.6812 Evaluate side-chains 273 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 26 optimal weight: 0.2980 chunk 138 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.0370 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN G 190 HIS ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119221 restraints weight = 30270.336| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.56 r_work: 0.3343 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20988 Z= 0.134 Angle : 0.548 9.231 28554 Z= 0.284 Chirality : 0.040 0.158 3326 Planarity : 0.004 0.046 3476 Dihedral : 13.699 135.364 3198 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.36 % Allowed : 11.16 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2458 helix: 1.48 (0.16), residues: 1144 sheet: -0.75 (0.23), residues: 497 loop : -0.49 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 44 TYR 0.019 0.001 TYR B 186 PHE 0.024 0.001 PHE F 245 TRP 0.020 0.001 TRP A 327 HIS 0.008 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00305 (20988) covalent geometry : angle 0.54830 (28554) hydrogen bonds : bond 0.04173 ( 1029) hydrogen bonds : angle 4.90251 ( 2937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.776 Fit side-chains REVERT: A 318 MET cc_start: 0.7919 (tpt) cc_final: 0.7256 (tpp) REVERT: A 322 ASN cc_start: 0.7944 (m-40) cc_final: 0.7531 (m-40) REVERT: A 467 ASP cc_start: 0.7718 (p0) cc_final: 0.7489 (p0) REVERT: C 99 ASP cc_start: 0.7743 (m-30) cc_final: 0.7511 (m-30) REVERT: E 119 MET cc_start: 0.6345 (mmm) cc_final: 0.5891 (mmm) REVERT: F 199 MSE cc_start: 0.5640 (mtt) cc_final: 0.1790 (tpt) outliers start: 30 outliers final: 19 residues processed: 314 average time/residue: 0.1453 time to fit residues: 71.0721 Evaluate side-chains 283 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 121 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 237 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 186 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 0.0980 chunk 192 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 636 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119695 restraints weight = 30386.883| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.45 r_work: 0.3342 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20988 Z= 0.120 Angle : 0.538 8.945 28554 Z= 0.277 Chirality : 0.039 0.152 3326 Planarity : 0.004 0.043 3476 Dihedral : 13.631 135.466 3198 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.68 % Allowed : 12.70 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2458 helix: 1.56 (0.16), residues: 1144 sheet: -0.76 (0.23), residues: 495 loop : -0.51 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 69 TYR 0.018 0.001 TYR B 186 PHE 0.023 0.001 PHE F 245 TRP 0.022 0.001 TRP A 327 HIS 0.010 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00270 (20988) covalent geometry : angle 0.53796 (28554) hydrogen bonds : bond 0.03726 ( 1029) hydrogen bonds : angle 4.69168 ( 2937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7930 (tpt) cc_final: 0.7279 (tpp) REVERT: A 322 ASN cc_start: 0.7931 (m-40) cc_final: 0.7496 (m-40) REVERT: C 99 ASP cc_start: 0.7793 (m-30) cc_final: 0.7547 (m-30) REVERT: E 119 MET cc_start: 0.6176 (mmm) cc_final: 0.5777 (mmm) REVERT: E 244 ASN cc_start: 0.5345 (m-40) cc_final: 0.5051 (m110) REVERT: F 199 MSE cc_start: 0.5662 (mtt) cc_final: 0.1883 (tpt) REVERT: G 113 GLU cc_start: 0.7517 (tp30) cc_final: 0.6812 (tt0) outliers start: 37 outliers final: 25 residues processed: 320 average time/residue: 0.1456 time to fit residues: 73.3637 Evaluate side-chains 287 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 407 HIS A 636 GLN B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116556 restraints weight = 30512.128| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.45 r_work: 0.3287 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20988 Z= 0.202 Angle : 0.579 8.707 28554 Z= 0.297 Chirality : 0.042 0.171 3326 Planarity : 0.004 0.046 3476 Dihedral : 13.740 137.596 3198 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.04 % Allowed : 13.79 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2458 helix: 1.46 (0.16), residues: 1148 sheet: -0.81 (0.23), residues: 496 loop : -0.51 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 69 TYR 0.018 0.002 TYR D 31 PHE 0.021 0.002 PHE F 245 TRP 0.024 0.002 TRP A 327 HIS 0.010 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00480 (20988) covalent geometry : angle 0.57850 (28554) hydrogen bonds : bond 0.04176 ( 1029) hydrogen bonds : angle 4.71434 ( 2937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.887 Fit side-chains REVERT: A 318 MET cc_start: 0.7929 (tpt) cc_final: 0.7494 (tpp) REVERT: A 322 ASN cc_start: 0.7993 (m-40) cc_final: 0.7489 (m-40) REVERT: A 424 ASP cc_start: 0.7639 (t0) cc_final: 0.7123 (t0) REVERT: C 99 ASP cc_start: 0.7823 (m-30) cc_final: 0.7511 (m-30) REVERT: E 119 MET cc_start: 0.6191 (mmm) cc_final: 0.5882 (mmm) REVERT: E 244 ASN cc_start: 0.5592 (m-40) cc_final: 0.5252 (m110) REVERT: F 199 MSE cc_start: 0.5889 (mtt) cc_final: 0.2010 (tpt) REVERT: G 113 GLU cc_start: 0.7470 (tp30) cc_final: 0.6852 (tt0) REVERT: H 1 MSE cc_start: 0.5268 (pmm) cc_final: 0.4770 (ptp) REVERT: H 101 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8520 (pp) REVERT: H 169 PHE cc_start: 0.7541 (m-10) cc_final: 0.7308 (m-10) outliers start: 45 outliers final: 28 residues processed: 290 average time/residue: 0.1421 time to fit residues: 65.4207 Evaluate side-chains 277 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118500 restraints weight = 30299.171| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.43 r_work: 0.3316 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20988 Z= 0.143 Angle : 0.553 9.402 28554 Z= 0.285 Chirality : 0.040 0.186 3326 Planarity : 0.004 0.047 3476 Dihedral : 13.666 136.248 3198 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.72 % Allowed : 15.06 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2458 helix: 1.57 (0.16), residues: 1141 sheet: -0.81 (0.23), residues: 501 loop : -0.46 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 69 TYR 0.020 0.001 TYR B 186 PHE 0.021 0.001 PHE F 245 TRP 0.026 0.001 TRP A 327 HIS 0.011 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00331 (20988) covalent geometry : angle 0.55310 (28554) hydrogen bonds : bond 0.03723 ( 1029) hydrogen bonds : angle 4.57983 ( 2937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 271 time to evaluate : 0.820 Fit side-chains REVERT: A 318 MET cc_start: 0.7943 (tpt) cc_final: 0.7398 (tpt) REVERT: A 322 ASN cc_start: 0.7977 (m-40) cc_final: 0.7735 (m-40) REVERT: A 424 ASP cc_start: 0.7594 (t0) cc_final: 0.7080 (t0) REVERT: C 99 ASP cc_start: 0.7812 (m-30) cc_final: 0.7506 (m-30) REVERT: E 244 ASN cc_start: 0.5530 (m-40) cc_final: 0.5193 (m110) REVERT: F 199 MSE cc_start: 0.5951 (mtt) cc_final: 0.2093 (tpt) REVERT: G 113 GLU cc_start: 0.7340 (tp30) cc_final: 0.6741 (tt0) REVERT: H 1 MSE cc_start: 0.5067 (pmm) cc_final: 0.4770 (ptp) REVERT: H 101 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8566 (pp) outliers start: 38 outliers final: 27 residues processed: 294 average time/residue: 0.1548 time to fit residues: 70.8709 Evaluate side-chains 274 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 159 ASN Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 6 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 24 optimal weight: 0.0270 chunk 184 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119861 restraints weight = 30247.724| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.44 r_work: 0.3337 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20988 Z= 0.117 Angle : 0.541 10.029 28554 Z= 0.277 Chirality : 0.039 0.170 3326 Planarity : 0.003 0.047 3476 Dihedral : 13.558 136.056 3198 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.81 % Allowed : 15.34 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2458 helix: 1.61 (0.16), residues: 1153 sheet: -0.69 (0.23), residues: 490 loop : -0.44 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.028 0.001 TYR A 352 PHE 0.025 0.001 PHE H 248 TRP 0.031 0.002 TRP A 327 HIS 0.012 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00262 (20988) covalent geometry : angle 0.54139 (28554) hydrogen bonds : bond 0.03413 ( 1029) hydrogen bonds : angle 4.44354 ( 2937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7899 (tpt) cc_final: 0.7402 (tpp) REVERT: A 322 ASN cc_start: 0.7937 (m-40) cc_final: 0.7258 (m110) REVERT: A 424 ASP cc_start: 0.7588 (t0) cc_final: 0.7033 (t0) REVERT: C 99 ASP cc_start: 0.7794 (m-30) cc_final: 0.7512 (m-30) REVERT: E 119 MET cc_start: 0.6455 (mmm) cc_final: 0.6185 (mmm) REVERT: E 184 ARG cc_start: 0.8612 (ptp-110) cc_final: 0.8335 (ptp-170) REVERT: E 244 ASN cc_start: 0.5448 (m-40) cc_final: 0.5110 (m110) REVERT: F 199 MSE cc_start: 0.5984 (mtt) cc_final: 0.2168 (tpt) REVERT: G 113 GLU cc_start: 0.7336 (tp30) cc_final: 0.6805 (tt0) REVERT: H 101 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8511 (pp) outliers start: 40 outliers final: 30 residues processed: 302 average time/residue: 0.1463 time to fit residues: 69.5660 Evaluate side-chains 289 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 23 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 184 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 175 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120006 restraints weight = 30099.569| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.47 r_work: 0.3338 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20988 Z= 0.117 Angle : 0.542 11.977 28554 Z= 0.277 Chirality : 0.040 0.166 3326 Planarity : 0.004 0.052 3476 Dihedral : 13.515 136.144 3198 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.00 % Allowed : 15.43 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2458 helix: 1.66 (0.16), residues: 1149 sheet: -0.67 (0.23), residues: 502 loop : -0.35 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 69 TYR 0.021 0.001 TYR B 186 PHE 0.021 0.001 PHE F 245 TRP 0.030 0.002 TRP A 327 HIS 0.012 0.001 HIS H 64 Details of bonding type rmsd covalent geometry : bond 0.00267 (20988) covalent geometry : angle 0.54237 (28554) hydrogen bonds : bond 0.03381 ( 1029) hydrogen bonds : angle 4.38912 ( 2937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7903 (tpt) cc_final: 0.7441 (tpp) REVERT: A 322 ASN cc_start: 0.7945 (m-40) cc_final: 0.7345 (m-40) REVERT: A 424 ASP cc_start: 0.7572 (t0) cc_final: 0.7006 (t0) REVERT: C 99 ASP cc_start: 0.7800 (m-30) cc_final: 0.7523 (m-30) REVERT: E 184 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8340 (ptp-170) REVERT: E 244 ASN cc_start: 0.5511 (m-40) cc_final: 0.5163 (m110) REVERT: F 199 MSE cc_start: 0.6012 (mtt) cc_final: 0.2185 (tpt) REVERT: G 113 GLU cc_start: 0.7311 (tp30) cc_final: 0.6801 (tt0) REVERT: H 101 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8495 (pp) outliers start: 44 outliers final: 34 residues processed: 309 average time/residue: 0.1469 time to fit residues: 71.3604 Evaluate side-chains 303 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 268 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 246 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 206 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.153461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118753 restraints weight = 30037.674| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.45 r_work: 0.3319 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20988 Z= 0.144 Angle : 0.563 13.253 28554 Z= 0.287 Chirality : 0.040 0.186 3326 Planarity : 0.004 0.055 3476 Dihedral : 13.541 137.022 3198 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.00 % Allowed : 15.74 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2458 helix: 1.65 (0.16), residues: 1148 sheet: -0.65 (0.23), residues: 501 loop : -0.43 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.024 0.001 TYR A 352 PHE 0.020 0.001 PHE F 245 TRP 0.032 0.002 TRP A 327 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00338 (20988) covalent geometry : angle 0.56279 (28554) hydrogen bonds : bond 0.03565 ( 1029) hydrogen bonds : angle 4.42291 ( 2937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7899 (tpt) cc_final: 0.7430 (tpp) REVERT: A 322 ASN cc_start: 0.7986 (m-40) cc_final: 0.7375 (m-40) REVERT: A 424 ASP cc_start: 0.7575 (t0) cc_final: 0.7012 (t0) REVERT: C 99 ASP cc_start: 0.7818 (m-30) cc_final: 0.7522 (m-30) REVERT: E 119 MET cc_start: 0.6631 (mmm) cc_final: 0.5980 (mmt) REVERT: E 184 ARG cc_start: 0.8657 (ptp-110) cc_final: 0.8401 (ptp-170) REVERT: E 244 ASN cc_start: 0.5619 (m-40) cc_final: 0.5244 (m110) REVERT: F 199 MSE cc_start: 0.6007 (mtt) cc_final: 0.2181 (tpt) REVERT: G 113 GLU cc_start: 0.7321 (tp30) cc_final: 0.6864 (tt0) REVERT: H 101 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8527 (pp) REVERT: H 214 ASP cc_start: 0.7993 (m-30) cc_final: 0.7611 (m-30) outliers start: 44 outliers final: 33 residues processed: 303 average time/residue: 0.1522 time to fit residues: 71.7005 Evaluate side-chains 297 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 246 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN E 227 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119555 restraints weight = 30160.188| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.49 r_work: 0.3332 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20988 Z= 0.126 Angle : 0.560 13.715 28554 Z= 0.285 Chirality : 0.040 0.222 3326 Planarity : 0.004 0.055 3476 Dihedral : 13.526 136.016 3198 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.63 % Allowed : 16.52 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2458 helix: 1.68 (0.16), residues: 1148 sheet: -0.60 (0.23), residues: 501 loop : -0.44 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 69 TYR 0.023 0.001 TYR A 352 PHE 0.021 0.001 PHE F 245 TRP 0.035 0.002 TRP A 327 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00291 (20988) covalent geometry : angle 0.56022 (28554) hydrogen bonds : bond 0.03404 ( 1029) hydrogen bonds : angle 4.38329 ( 2937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7870 (tpt) cc_final: 0.7419 (tpp) REVERT: A 322 ASN cc_start: 0.7986 (m-40) cc_final: 0.7363 (m-40) REVERT: A 424 ASP cc_start: 0.7585 (t0) cc_final: 0.7021 (t0) REVERT: C 99 ASP cc_start: 0.7810 (m-30) cc_final: 0.7521 (m-30) REVERT: E 119 MET cc_start: 0.6631 (mmm) cc_final: 0.6080 (mmm) REVERT: E 184 ARG cc_start: 0.8626 (ptp-110) cc_final: 0.8372 (ptp-170) REVERT: E 244 ASN cc_start: 0.5583 (m-40) cc_final: 0.5211 (m110) REVERT: F 199 MSE cc_start: 0.5978 (mtt) cc_final: 0.2262 (tpt) REVERT: G 80 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.8008 (mmm160) REVERT: G 113 GLU cc_start: 0.7287 (tp30) cc_final: 0.6826 (tt0) REVERT: H 101 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8531 (pp) REVERT: H 214 ASP cc_start: 0.7985 (m-30) cc_final: 0.7587 (m-30) outliers start: 36 outliers final: 32 residues processed: 304 average time/residue: 0.1512 time to fit residues: 72.2629 Evaluate side-chains 304 residues out of total 2204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 191 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 232 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 407 HIS B 102 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115616 restraints weight = 30076.669| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.68 r_work: 0.3326 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20988 Z= 0.150 Angle : 0.724 59.191 28554 Z= 0.411 Chirality : 0.040 0.392 3326 Planarity : 0.004 0.055 3476 Dihedral : 13.533 136.033 3198 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 1.72 % Allowed : 16.61 % Favored : 81.67 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2458 helix: 1.68 (0.16), residues: 1148 sheet: -0.60 (0.23), residues: 501 loop : -0.44 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 69 TYR 0.020 0.001 TYR A 352 PHE 0.021 0.001 PHE F 245 TRP 0.031 0.002 TRP A 327 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00316 (20988) covalent geometry : angle 0.72431 (28554) hydrogen bonds : bond 0.03402 ( 1029) hydrogen bonds : angle 4.38338 ( 2937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4670.45 seconds wall clock time: 81 minutes 1.82 seconds (4861.82 seconds total)