Starting phenix.real_space_refine on Wed Mar 4 21:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.map" model { file = "/net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r4h_14312/03_2026/7r4h_14312.cif" } resolution = 2.34 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 10476 2.51 5 N 2801 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s 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: 16485 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.21 Number of scatterers: 16485 At special positions: 0 Unit cell: (122.4, 132.3, 130.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 7 15.00 Mg 2 11.99 O 3102 8.00 N 2801 7.00 C 10476 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 783.3 milliseconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3928 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 57.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 26 through 43 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.643A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.534A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 99 through 112 removed outlier: 3.559A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.766A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 3.734A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.880A pdb=" N THR B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 3.826A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.890A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.588A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.653A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.563A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 250' Processing helix chain 'B' and resid 252 through 267 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.900A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.776A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.545A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.506A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.572A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 469 through 476 removed outlier: 4.323A pdb=" N GLY B 472 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 476 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 495 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.568A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.620A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.678A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.638A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.527A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.243A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 145 through 148 removed outlier: 3.818A pdb=" N LEU C 148 " --> pdb=" O LEU C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 145 through 148' Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'G' and resid 6 through 16 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.684A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 66 through 75 Processing helix chain 'G' and resid 78 through 93 Processing helix chain 'G' and resid 99 through 102 Processing helix chain 'G' and resid 103 through 112 removed outlier: 3.759A pdb=" N ASN G 112 " --> pdb=" O LYS G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 133 through 138 removed outlier: 4.112A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 removed outlier: 3.586A pdb=" N LEU G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 168 removed outlier: 3.895A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 180 Proline residue: G 177 - end of helix removed outlier: 3.579A pdb=" N LYS G 180 " --> pdb=" O PRO G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 205 Processing helix chain 'G' and resid 211 through 214 removed outlier: 4.032A pdb=" N LYS G 214 " --> pdb=" O HIS G 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 214' Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 242 through 256 Processing helix chain 'G' and resid 261 through 278 removed outlier: 4.597A pdb=" N ASP G 269 " --> pdb=" O GLU G 265 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR G 278 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 299 Processing helix chain 'G' and resid 302 through 318 removed outlier: 3.570A pdb=" N VAL G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 335 Processing helix chain 'G' and resid 339 through 344 removed outlier: 3.753A pdb=" N GLN G 344 " --> pdb=" O HIS G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 355 removed outlier: 3.864A pdb=" N LYS G 355 " --> pdb=" O VAL G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 372 Processing helix chain 'G' and resid 377 through 391 removed outlier: 4.067A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 411 Processing helix chain 'G' and resid 414 through 429 Processing helix chain 'G' and resid 430 through 433 Processing helix chain 'G' and resid 434 through 436 No H-bonds generated for 'chain 'G' and resid 434 through 436' Processing helix chain 'G' and resid 437 through 448 Processing helix chain 'G' and resid 452 through 466 Processing helix chain 'G' and resid 469 through 488 removed outlier: 3.643A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 515 Processing helix chain 'G' and resid 521 through 537 removed outlier: 4.259A pdb=" N THR G 535 " --> pdb=" O MET G 531 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 536 " --> pdb=" O LYS G 532 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 550 Processing helix chain 'G' and resid 556 through 573 Processing helix chain 'G' and resid 576 through 581 removed outlier: 3.552A pdb=" N LEU G 580 " --> pdb=" O MET G 576 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 74 through 82 removed outlier: 3.604A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 82 " --> pdb=" O ARG H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 111 Processing helix chain 'H' and resid 135 through 144 Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 165 through 176 Processing helix chain 'M' and resid 28 through 31 removed outlier: 4.191A pdb=" N GLU M 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 31' Processing helix chain 'M' and resid 32 through 43 removed outlier: 3.643A pdb=" N ILE M 36 " --> pdb=" O HIS M 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 95 Processing helix chain 'M' and resid 100 through 106 removed outlier: 4.393A pdb=" N ARG M 104 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP M 105 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN M 106 " --> pdb=" O SER M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 100 through 106' Processing helix chain 'M' and resid 106 through 117 Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 150 through 154 removed outlier: 3.577A pdb=" N VAL M 153 " --> pdb=" O PRO M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 243 through 251 Processing helix chain 'S' and resid 24 through 41 Processing helix chain 'S' and resid 76 through 96 Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.841A pdb=" N ILE S 103 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 128 through 142 removed outlier: 3.608A pdb=" N VAL S 132 " --> pdb=" O LYS S 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN S 142 " --> pdb=" O SER S 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 58 removed outlier: 3.758A pdb=" N TYR C 58 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 61 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET C 18 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 64 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 236 through 237 removed outlier: 3.601A pdb=" N ILE G 240 " --> pdb=" O VAL G 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 51 through 57 removed outlier: 6.478A pdb=" N MET H 18 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TRP H 66 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE H 20 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL H 68 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET H 22 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG H 19 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE H 89 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU H 21 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL H 91 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 23 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP H 93 " --> pdb=" O VAL H 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 15 through 20 removed outlier: 6.948A pdb=" N VAL M 8 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N CYS M 18 " --> pdb=" O VAL M 6 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL M 6 " --> pdb=" O CYS M 18 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'M' and resid 235 through 238 removed outlier: 5.403A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 181 " --> pdb=" O GLY M 416 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR M 418 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL M 183 " --> pdb=" O TYR M 418 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU M 420 " --> pdb=" O VAL M 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 235 through 238 removed outlier: 5.403A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 181 " --> pdb=" O GLY M 416 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR M 418 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL M 183 " --> pdb=" O TYR M 418 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU M 420 " --> pdb=" O VAL M 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 253 through 255 removed outlier: 4.234A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR M 394 " --> pdb=" O GLY M 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 277 through 286 removed outlier: 3.666A pdb=" N ARG M 290 " --> pdb=" O HIS M 286 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE M 291 " --> pdb=" O PHE M 360 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY M 361 " --> pdb=" O SER M 322 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER M 322 " --> pdb=" O GLY M 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 306 through 315 removed outlier: 6.545A pdb=" N THR M 306 " --> pdb=" O PRO M 349 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN M 308 " --> pdb=" O SER M 347 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER M 347 " --> pdb=" O ASN M 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.373A pdb=" N LEU S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE S 5 " --> pdb=" O GLN S 17 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP S 19 " --> pdb=" O HIS S 3 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE S 4 " --> pdb=" O ALA S 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 118 through 119 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4636 1.34 - 1.46: 2967 1.46 - 1.58: 8983 1.58 - 1.70: 23 1.70 - 1.82: 158 Bond restraints: 16767 Sorted by residual: bond pdb=" CB ASN G 341 " pdb=" CG ASN G 341 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.41e+00 bond pdb=" C ARG C 75 " pdb=" N PRO C 76 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.22e+00 bond pdb=" CA ASN G 377 " pdb=" CB ASN G 377 " ideal model delta sigma weight residual 1.526 1.566 -0.040 1.68e-02 3.54e+03 5.74e+00 bond pdb=" CG1 ILE S 135 " pdb=" CD1 ILE S 135 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.42e+00 bond pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 1.520 1.589 -0.069 3.00e-02 1.11e+03 5.34e+00 ... (remaining 16762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 22354 4.26 - 8.52: 270 8.52 - 12.77: 50 12.77 - 17.03: 8 17.03 - 21.29: 4 Bond angle restraints: 22686 Sorted by residual: angle pdb=" CB LYS B 26 " pdb=" CG LYS B 26 " pdb=" CD LYS B 26 " ideal model delta sigma weight residual 111.30 126.40 -15.10 2.30e+00 1.89e-01 4.31e+01 angle pdb=" CA LEU G 406 " pdb=" CB LEU G 406 " pdb=" CG LEU G 406 " ideal model delta sigma weight residual 116.30 137.59 -21.29 3.50e+00 8.16e-02 3.70e+01 angle pdb=" CA LYS G 546 " pdb=" CB LYS G 546 " pdb=" CG LYS G 546 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.56e+01 angle pdb=" CA GLU G 393 " pdb=" CB GLU G 393 " pdb=" CG GLU G 393 " ideal model delta sigma weight residual 114.10 126.01 -11.91 2.00e+00 2.50e-01 3.55e+01 angle pdb=" CA LYS G 383 " pdb=" CB LYS G 383 " pdb=" CG LYS G 383 " ideal model delta sigma weight residual 114.10 125.89 -11.79 2.00e+00 2.50e-01 3.48e+01 ... (remaining 22681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 9745 33.84 - 67.68: 502 67.68 - 101.52: 34 101.52 - 135.35: 3 135.35 - 169.19: 2 Dihedral angle restraints: 10286 sinusoidal: 4244 harmonic: 6042 Sorted by residual: dihedral pdb=" CA ASN C 175 " pdb=" C ASN C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual 180.00 143.91 36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" C5' GTP H1001 " pdb=" O5' GTP H1001 " pdb=" PA GTP H1001 " pdb=" O3A GTP H1001 " ideal model delta sinusoidal sigma weight residual 69.27 -99.92 169.19 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C1001 " pdb=" O5' GTP C1001 " pdb=" PA GTP C1001 " pdb=" O3A GTP C1001 " ideal model delta sinusoidal sigma weight residual 69.27 -132.85 -157.88 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 10283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2251 0.084 - 0.168: 323 0.168 - 0.251: 39 0.251 - 0.335: 5 0.335 - 0.419: 3 Chirality restraints: 2621 Sorted by residual: chirality pdb=" CG LEU G 256 " pdb=" CB LEU G 256 " pdb=" CD1 LEU G 256 " pdb=" CD2 LEU G 256 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL G 512 " pdb=" CA VAL G 512 " pdb=" CG1 VAL G 512 " pdb=" CG2 VAL G 512 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE G 550 " pdb=" CA ILE G 550 " pdb=" CG1 ILE G 550 " pdb=" CG2 ILE G 550 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2618 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 104 " 0.358 9.50e-02 1.11e+02 1.61e-01 1.84e+01 pdb=" NE ARG C 104 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 104 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 104 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL M 316 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO M 317 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO M 317 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 317 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 46 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO C 47 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.039 5.00e-02 4.00e+02 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 352 2.67 - 3.23: 14030 3.23 - 3.79: 27714 3.79 - 4.34: 36678 4.34 - 4.90: 59734 Nonbonded interactions: 138508 Sorted by model distance: nonbonded pdb=" O2A GTP H1001 " pdb="MG MG H1002 " model vdw 2.119 2.170 nonbonded pdb=" O3A GTP C1001 " pdb="MG MG C1002 " model vdw 2.140 2.170 nonbonded pdb=" O3A GTP H1001 " pdb="MG MG H1002 " model vdw 2.160 2.170 nonbonded pdb=" O3G GTP C1001 " pdb="MG MG C1002 " model vdw 2.165 2.170 nonbonded pdb=" O VAL G 327 " pdb=" OG SER G 331 " model vdw 2.283 3.040 ... (remaining 138503 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 'C' and (resid 17 through 179 or resid 1001 through 1002)) 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.100 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:9.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.006 0.091 16772 Z= 0.281 Angle : 1.223 21.290 22686 Z= 0.620 Chirality : 0.060 0.419 2621 Planarity : 0.009 0.161 2870 Dihedral : 19.220 169.193 6358 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.93 % Allowed : 33.01 % Favored : 63.06 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.26 (0.15), residues: 2031 helix: -2.48 (0.11), residues: 1084 sheet: -1.06 (0.33), residues: 255 loop : -1.64 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG C 104 TYR 0.042 0.002 TYR H 58 PHE 0.018 0.003 PHE S 4 TRP 0.035 0.003 TRP C 172 HIS 0.008 0.001 HIS G 340 Details of bonding type rmsd covalent geometry : bond 0.00616 (16767) covalent geometry : angle 1.22311 (22686) hydrogen bonds : bond 0.13003 ( 864) hydrogen bonds : angle 7.25673 ( 2616) Misc. bond : bond 0.00364 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 GLU cc_start: 0.7534 (pm20) cc_final: 0.7322 (pm20) REVERT: G 265 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8542 (pp20) REVERT: G 450 GLU cc_start: 0.7726 (pm20) cc_final: 0.7467 (pm20) REVERT: M 303 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7454 (mtp85) REVERT: S 59 TYR cc_start: 0.8848 (p90) cc_final: 0.8630 (p90) outliers start: 72 outliers final: 56 residues processed: 249 average time/residue: 0.5421 time to fit residues: 150.8560 Evaluate side-chains 229 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 399 ASP Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 554 SER Chi-restraints excluded: chain G residue 564 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 303 ARG Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 401 SER Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 48 SER Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS G 112 ASN G 283 ASN M 89 GLN M 288 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078963 restraints weight = 28911.901| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.49 r_work: 0.3095 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16772 Z= 0.135 Angle : 0.625 11.766 22686 Z= 0.317 Chirality : 0.043 0.182 2621 Planarity : 0.005 0.053 2870 Dihedral : 9.899 170.658 2342 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.86 % Allowed : 27.65 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.17), residues: 2031 helix: -0.58 (0.14), residues: 1103 sheet: -0.57 (0.31), residues: 258 loop : -1.16 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.025 0.001 TYR H 58 PHE 0.014 0.001 PHE S 67 TRP 0.018 0.001 TRP C 172 HIS 0.003 0.001 HIS G 418 Details of bonding type rmsd covalent geometry : bond 0.00302 (16767) covalent geometry : angle 0.62535 (22686) hydrogen bonds : bond 0.03938 ( 864) hydrogen bonds : angle 4.86843 ( 2616) Misc. bond : bond 0.00164 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 176 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7736 (tptp) cc_final: 0.7393 (tptp) REVERT: B 91 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: B 469 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6294 (t80) REVERT: C 55 THR cc_start: 0.8846 (m) cc_final: 0.8573 (t) REVERT: C 108 MET cc_start: 0.7162 (mmt) cc_final: 0.6869 (mmm) REVERT: H 58 TYR cc_start: 0.7902 (t80) cc_final: 0.7608 (t80) REVERT: H 86 GLN cc_start: 0.9022 (mt0) cc_final: 0.8818 (mt0) REVERT: H 105 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7982 (mm-30) REVERT: L 359 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: L 365 ILE cc_start: 0.7396 (pp) cc_final: 0.7040 (mt) REVERT: M 225 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7562 (ptp-170) REVERT: M 345 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8116 (t) REVERT: S 25 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (t0) outliers start: 89 outliers final: 35 residues processed: 246 average time/residue: 0.6185 time to fit residues: 168.2596 Evaluate side-chains 199 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 225 ARG Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 99 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 176 GLN M 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.077806 restraints weight = 29166.324| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.48 r_work: 0.3070 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16772 Z= 0.129 Angle : 0.598 16.302 22686 Z= 0.299 Chirality : 0.042 0.160 2621 Planarity : 0.004 0.046 2870 Dihedral : 9.229 171.157 2285 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.41 % Allowed : 25.96 % Favored : 68.63 % 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: -0.45 (0.18), residues: 2031 helix: 0.23 (0.15), residues: 1109 sheet: -0.43 (0.32), residues: 260 loop : -0.92 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 304 TYR 0.016 0.001 TYR H 58 PHE 0.012 0.001 PHE G 117 TRP 0.015 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00292 (16767) covalent geometry : angle 0.59797 (22686) hydrogen bonds : bond 0.03624 ( 864) hydrogen bonds : angle 4.51968 ( 2616) Misc. bond : bond 0.00176 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 179 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7949 (tptp) cc_final: 0.7739 (tptp) REVERT: B 469 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6229 (t80) REVERT: B 567 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8508 (mt) REVERT: C 55 THR cc_start: 0.8895 (m) cc_final: 0.8617 (t) REVERT: C 108 MET cc_start: 0.7116 (mmt) cc_final: 0.6841 (mmm) REVERT: G 381 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6941 (mpt) REVERT: G 546 LYS cc_start: 0.7915 (pptt) cc_final: 0.7619 (pptt) REVERT: H 58 TYR cc_start: 0.8111 (t80) cc_final: 0.7793 (t80) REVERT: H 86 GLN cc_start: 0.9024 (mt0) cc_final: 0.8806 (mt0) REVERT: H 104 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7226 (ttp-110) REVERT: H 105 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7640 (mm-30) REVERT: L 359 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6386 (tm-30) REVERT: L 360 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: L 365 ILE cc_start: 0.7244 (pp) cc_final: 0.6897 (mt) REVERT: M 177 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: M 209 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: M 345 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8228 (t) REVERT: S 16 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8731 (tp) REVERT: S 25 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8268 (t0) REVERT: S 45 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7884 (pmm150) outliers start: 99 outliers final: 40 residues processed: 253 average time/residue: 0.5968 time to fit residues: 167.6864 Evaluate side-chains 214 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 360 GLU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 345 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 123 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 176 GLN G 100 HIS G 340 HIS H 152 ASN M 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078330 restraints weight = 28912.860| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.47 r_work: 0.3087 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16772 Z= 0.107 Angle : 0.572 14.494 22686 Z= 0.284 Chirality : 0.042 0.177 2621 Planarity : 0.004 0.042 2870 Dihedral : 9.012 172.064 2281 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.14 % Allowed : 25.52 % Favored : 69.34 % 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: -0.10 (0.18), residues: 2031 helix: 0.59 (0.16), residues: 1111 sheet: -0.37 (0.32), residues: 254 loop : -0.89 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 304 TYR 0.014 0.001 TYR H 58 PHE 0.011 0.001 PHE G 117 TRP 0.018 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00236 (16767) covalent geometry : angle 0.57169 (22686) hydrogen bonds : bond 0.03333 ( 864) hydrogen bonds : angle 4.33767 ( 2616) Misc. bond : bond 0.00165 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 172 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8039 (tptp) cc_final: 0.7802 (tptp) REVERT: B 58 MET cc_start: 0.9155 (ttt) cc_final: 0.8845 (ttt) REVERT: B 60 THR cc_start: 0.8663 (p) cc_final: 0.8219 (t) REVERT: B 469 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6165 (t80) REVERT: B 567 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8503 (mt) REVERT: C 55 THR cc_start: 0.8904 (m) cc_final: 0.8602 (t) REVERT: C 108 MET cc_start: 0.7197 (mmt) cc_final: 0.6923 (mmm) REVERT: C 176 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: G 133 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7790 (mp0) REVERT: G 379 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8368 (mtp85) REVERT: G 381 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7106 (mpt) REVERT: G 546 LYS cc_start: 0.7932 (pptt) cc_final: 0.7640 (pptt) REVERT: H 86 GLN cc_start: 0.9014 (mt0) cc_final: 0.8804 (mt0) REVERT: H 104 ARG cc_start: 0.7898 (ttt90) cc_final: 0.7322 (ttp-110) REVERT: H 105 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7638 (mm-30) REVERT: H 130 LEU cc_start: 0.7648 (pt) cc_final: 0.7399 (pp) REVERT: L 359 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: L 365 ILE cc_start: 0.7226 (pp) cc_final: 0.6889 (mt) REVERT: M 177 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: M 209 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: S 16 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (tp) REVERT: S 25 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8277 (t0) REVERT: S 26 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8890 (mppt) REVERT: S 45 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7773 (pmm150) outliers start: 94 outliers final: 39 residues processed: 246 average time/residue: 0.6017 time to fit residues: 163.9527 Evaluate side-chains 215 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 0.0570 chunk 70 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN C 132 ASN G 218 GLN G 340 HIS M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.109976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077234 restraints weight = 28840.200| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.50 r_work: 0.3063 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16772 Z= 0.124 Angle : 0.582 13.602 22686 Z= 0.288 Chirality : 0.043 0.220 2621 Planarity : 0.004 0.042 2870 Dihedral : 8.981 171.194 2277 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.70 % Allowed : 25.90 % Favored : 69.40 % 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: 0.14 (0.19), residues: 2031 helix: 0.78 (0.16), residues: 1110 sheet: -0.40 (0.32), residues: 258 loop : -0.72 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 304 TYR 0.022 0.001 TYR H 58 PHE 0.012 0.001 PHE G 117 TRP 0.020 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00282 (16767) covalent geometry : angle 0.58162 (22686) hydrogen bonds : bond 0.03405 ( 864) hydrogen bonds : angle 4.27420 ( 2616) Misc. bond : bond 0.00173 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 167 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8106 (tptp) cc_final: 0.7833 (tptp) REVERT: B 60 THR cc_start: 0.8674 (p) cc_final: 0.8224 (t) REVERT: B 469 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6279 (t80) REVERT: B 567 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8489 (mt) REVERT: C 55 THR cc_start: 0.8915 (m) cc_final: 0.8606 (t) REVERT: C 108 MET cc_start: 0.7290 (mmt) cc_final: 0.7004 (mmm) REVERT: G 133 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7849 (mp0) REVERT: G 180 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8191 (mmpt) REVERT: G 379 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8309 (mtp85) REVERT: G 450 GLU cc_start: 0.7894 (pm20) cc_final: 0.7579 (pm20) REVERT: G 546 LYS cc_start: 0.7930 (pptt) cc_final: 0.7616 (pptt) REVERT: H 86 GLN cc_start: 0.9046 (mt0) cc_final: 0.8820 (mt0) REVERT: H 104 ARG cc_start: 0.7874 (ttt90) cc_final: 0.7302 (ttp-110) REVERT: H 105 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7657 (mm-30) REVERT: L 359 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: L 365 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6888 (mt) REVERT: M 177 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: M 209 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: S 16 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (tp) REVERT: S 25 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8299 (t0) REVERT: S 26 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8901 (mppt) REVERT: S 45 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7865 (pmm150) outliers start: 86 outliers final: 45 residues processed: 233 average time/residue: 0.5909 time to fit residues: 152.5051 Evaluate side-chains 221 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 180 LYS Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 300 LYS Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 132 ASN C 152 ASN C 176 GLN G 340 HIS M 20 ASN S 3 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.106609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.073673 restraints weight = 28760.241| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.45 r_work: 0.2983 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16772 Z= 0.186 Angle : 0.626 12.624 22686 Z= 0.312 Chirality : 0.045 0.198 2621 Planarity : 0.004 0.042 2870 Dihedral : 9.183 166.933 2276 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.97 % Allowed : 25.41 % Favored : 69.62 % 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: 0.20 (0.19), residues: 2031 helix: 0.81 (0.16), residues: 1107 sheet: -0.36 (0.32), residues: 257 loop : -0.66 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 304 TYR 0.026 0.002 TYR H 58 PHE 0.015 0.002 PHE G 117 TRP 0.018 0.001 TRP C 172 HIS 0.007 0.001 HIS S 3 Details of bonding type rmsd covalent geometry : bond 0.00436 (16767) covalent geometry : angle 0.62648 (22686) hydrogen bonds : bond 0.03849 ( 864) hydrogen bonds : angle 4.40874 ( 2616) Misc. bond : bond 0.00200 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 168 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8185 (tptp) cc_final: 0.7852 (tptp) REVERT: B 60 THR cc_start: 0.8717 (p) cc_final: 0.8275 (t) REVERT: B 460 ASP cc_start: 0.8011 (m-30) cc_final: 0.7337 (p0) REVERT: B 469 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7193 (t80) REVERT: B 476 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6617 (ptpp) REVERT: C 55 THR cc_start: 0.8982 (m) cc_final: 0.8701 (t) REVERT: C 108 MET cc_start: 0.7533 (mmt) cc_final: 0.7247 (mmm) REVERT: G 133 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7826 (mp0) REVERT: G 180 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8125 (mmpt) REVERT: G 450 GLU cc_start: 0.7796 (pm20) cc_final: 0.7435 (pm20) REVERT: G 546 LYS cc_start: 0.8010 (pptt) cc_final: 0.7686 (pptt) REVERT: H 86 GLN cc_start: 0.9138 (mt0) cc_final: 0.8905 (mt0) REVERT: H 104 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7419 (ttp-110) REVERT: H 105 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7852 (mm-30) REVERT: L 359 GLN cc_start: 0.6758 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: L 365 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6928 (mt) REVERT: M 41 GLU cc_start: 0.8579 (tt0) cc_final: 0.8103 (tm-30) REVERT: M 177 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: M 209 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: S 26 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8997 (mppt) outliers start: 91 outliers final: 41 residues processed: 241 average time/residue: 0.5820 time to fit residues: 155.9697 Evaluate side-chains 206 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 180 LYS Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain S residue 26 LYS Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 0.0670 chunk 131 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN C 132 ASN G 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.076069 restraints weight = 28602.742| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.43 r_work: 0.3031 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16772 Z= 0.115 Angle : 0.580 12.823 22686 Z= 0.288 Chirality : 0.043 0.223 2621 Planarity : 0.004 0.043 2870 Dihedral : 8.952 171.121 2274 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.88 % Allowed : 26.72 % Favored : 69.40 % 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: 0.31 (0.19), residues: 2031 helix: 0.93 (0.16), residues: 1108 sheet: -0.26 (0.32), residues: 257 loop : -0.67 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 167 TYR 0.026 0.001 TYR H 58 PHE 0.011 0.001 PHE G 117 TRP 0.017 0.001 TRP C 172 HIS 0.005 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00261 (16767) covalent geometry : angle 0.58015 (22686) hydrogen bonds : bond 0.03383 ( 864) hydrogen bonds : angle 4.27092 ( 2616) Misc. bond : bond 0.00158 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8236 (tptp) cc_final: 0.7912 (tptp) REVERT: B 60 THR cc_start: 0.8604 (p) cc_final: 0.8153 (t) REVERT: B 460 ASP cc_start: 0.7970 (m-30) cc_final: 0.7310 (p0) REVERT: B 469 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7293 (t80) REVERT: C 55 THR cc_start: 0.8958 (m) cc_final: 0.8663 (t) REVERT: C 108 MET cc_start: 0.7548 (mmt) cc_final: 0.7269 (mmm) REVERT: G 133 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7859 (mp0) REVERT: G 379 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8204 (mtp85) REVERT: G 381 MET cc_start: 0.7187 (mpt) cc_final: 0.6815 (mpt) REVERT: G 450 GLU cc_start: 0.7797 (pm20) cc_final: 0.7497 (pm20) REVERT: G 546 LYS cc_start: 0.7976 (pptt) cc_final: 0.7640 (pptt) REVERT: H 86 GLN cc_start: 0.9063 (mt0) cc_final: 0.8801 (mt0) REVERT: H 104 ARG cc_start: 0.7951 (ttt90) cc_final: 0.7411 (ttp-110) REVERT: H 105 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7878 (mm-30) REVERT: L 359 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: L 365 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6860 (mt) REVERT: M 41 GLU cc_start: 0.8582 (tt0) cc_final: 0.8131 (tm-30) REVERT: M 177 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: M 209 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: S 25 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8256 (t0) outliers start: 71 outliers final: 36 residues processed: 228 average time/residue: 0.6251 time to fit residues: 157.5456 Evaluate side-chains 204 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 197 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075348 restraints weight = 28781.815| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.46 r_work: 0.3005 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16772 Z= 0.143 Angle : 0.607 12.845 22686 Z= 0.300 Chirality : 0.044 0.217 2621 Planarity : 0.004 0.042 2870 Dihedral : 8.989 170.382 2274 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.72 % Allowed : 26.99 % Favored : 69.29 % 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: 0.37 (0.19), residues: 2031 helix: 0.96 (0.16), residues: 1107 sheet: -0.37 (0.31), residues: 262 loop : -0.57 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 28 TYR 0.027 0.001 TYR H 58 PHE 0.013 0.001 PHE G 117 TRP 0.017 0.001 TRP C 172 HIS 0.007 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00336 (16767) covalent geometry : angle 0.60722 (22686) hydrogen bonds : bond 0.03571 ( 864) hydrogen bonds : angle 4.29013 ( 2616) Misc. bond : bond 0.00176 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 160 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8253 (tptp) cc_final: 0.7204 (tptp) REVERT: B 60 THR cc_start: 0.8587 (p) cc_final: 0.8215 (t) REVERT: B 460 ASP cc_start: 0.8008 (m-30) cc_final: 0.7368 (p0) REVERT: B 498 GLU cc_start: 0.8402 (pm20) cc_final: 0.8035 (pm20) REVERT: C 55 THR cc_start: 0.8966 (m) cc_final: 0.8678 (t) REVERT: C 108 MET cc_start: 0.7632 (mmt) cc_final: 0.7351 (mmm) REVERT: G 133 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7811 (mp0) REVERT: G 340 HIS cc_start: 0.8368 (t70) cc_final: 0.8103 (t-90) REVERT: G 379 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8130 (mtp85) REVERT: G 381 MET cc_start: 0.7228 (mpt) cc_final: 0.6987 (mpt) REVERT: G 546 LYS cc_start: 0.7969 (pptt) cc_final: 0.7643 (pptt) REVERT: H 86 GLN cc_start: 0.9062 (mt0) cc_final: 0.8797 (mt0) REVERT: H 104 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7370 (ttp-110) REVERT: H 105 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7853 (mm-30) REVERT: L 359 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: L 365 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6813 (mt) REVERT: M 41 GLU cc_start: 0.8580 (tt0) cc_final: 0.8120 (tm-30) REVERT: M 177 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: M 209 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: M 399 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6253 (tm-30) outliers start: 68 outliers final: 43 residues processed: 214 average time/residue: 0.6244 time to fit residues: 147.2251 Evaluate side-chains 205 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain L residue 365 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 209 GLU Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 192 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 0.1980 chunk 186 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.108250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076074 restraints weight = 28842.247| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.46 r_work: 0.3019 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16772 Z= 0.126 Angle : 0.603 12.919 22686 Z= 0.297 Chirality : 0.043 0.185 2621 Planarity : 0.004 0.042 2870 Dihedral : 8.927 171.766 2274 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.28 % Allowed : 27.76 % Favored : 68.96 % 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: 0.42 (0.19), residues: 2031 helix: 0.98 (0.16), residues: 1111 sheet: -0.33 (0.31), residues: 262 loop : -0.52 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 304 TYR 0.028 0.001 TYR H 58 PHE 0.012 0.001 PHE G 117 TRP 0.015 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 Details of bonding type rmsd covalent geometry : bond 0.00291 (16767) covalent geometry : angle 0.60313 (22686) hydrogen bonds : bond 0.03435 ( 864) hydrogen bonds : angle 4.25102 ( 2616) Misc. bond : bond 0.00165 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8232 (tptp) cc_final: 0.7882 (tptp) REVERT: B 60 THR cc_start: 0.8619 (p) cc_final: 0.8238 (t) REVERT: B 460 ASP cc_start: 0.8005 (m-30) cc_final: 0.7388 (p0) REVERT: B 498 GLU cc_start: 0.8398 (pm20) cc_final: 0.8037 (pm20) REVERT: C 55 THR cc_start: 0.8968 (m) cc_final: 0.8678 (t) REVERT: C 108 MET cc_start: 0.7578 (mmt) cc_final: 0.7300 (mmm) REVERT: G 133 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7809 (mp0) REVERT: G 379 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8161 (mtp85) REVERT: G 381 MET cc_start: 0.7224 (mpt) cc_final: 0.6992 (mpt) REVERT: G 416 ARG cc_start: 0.8123 (tmt170) cc_final: 0.7826 (tmt170) REVERT: G 546 LYS cc_start: 0.7987 (pptt) cc_final: 0.7668 (pptt) REVERT: H 86 GLN cc_start: 0.9048 (mt0) cc_final: 0.8801 (mt0) REVERT: H 105 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7924 (mm-30) REVERT: L 359 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: M 41 GLU cc_start: 0.8560 (tt0) cc_final: 0.8109 (tm-30) REVERT: M 177 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: M 399 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6244 (tm-30) outliers start: 60 outliers final: 42 residues processed: 209 average time/residue: 0.6142 time to fit residues: 141.7628 Evaluate side-chains 201 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 172 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN G 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074277 restraints weight = 28747.796| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.45 r_work: 0.2976 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16772 Z= 0.164 Angle : 0.648 16.489 22686 Z= 0.317 Chirality : 0.044 0.159 2621 Planarity : 0.004 0.043 2870 Dihedral : 9.053 169.956 2274 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.11 % Allowed : 27.87 % Favored : 69.02 % 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: 0.39 (0.19), residues: 2031 helix: 0.97 (0.16), residues: 1110 sheet: -0.36 (0.31), residues: 262 loop : -0.54 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 304 TYR 0.030 0.002 TYR H 58 PHE 0.015 0.001 PHE B 469 TRP 0.016 0.001 TRP C 172 HIS 0.007 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00387 (16767) covalent geometry : angle 0.64801 (22686) hydrogen bonds : bond 0.03695 ( 864) hydrogen bonds : angle 4.33203 ( 2616) Misc. bond : bond 0.00187 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8117 (tptp) cc_final: 0.7757 (tptp) REVERT: B 60 THR cc_start: 0.8615 (p) cc_final: 0.8289 (t) REVERT: B 460 ASP cc_start: 0.8110 (m-30) cc_final: 0.7544 (p0) REVERT: B 498 GLU cc_start: 0.8395 (pm20) cc_final: 0.8099 (pm20) REVERT: C 55 THR cc_start: 0.8995 (m) cc_final: 0.8719 (t) REVERT: C 108 MET cc_start: 0.7651 (mmt) cc_final: 0.7384 (mmm) REVERT: G 56 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: G 133 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7837 (mp0) REVERT: G 379 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8064 (mtp85) REVERT: G 381 MET cc_start: 0.7219 (mpt) cc_final: 0.7015 (mpt) REVERT: G 416 ARG cc_start: 0.8041 (tmt170) cc_final: 0.7707 (tmt170) REVERT: G 546 LYS cc_start: 0.8002 (pptt) cc_final: 0.7720 (pptt) REVERT: H 105 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7962 (mm-30) REVERT: L 359 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: M 41 GLU cc_start: 0.8593 (tt0) cc_final: 0.8131 (tm-30) REVERT: M 177 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: M 399 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6270 (tm-30) outliers start: 57 outliers final: 41 residues processed: 205 average time/residue: 0.6072 time to fit residues: 138.0787 Evaluate side-chains 202 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 379 ARG Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain L residue 359 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 99 GLU Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 387 THR Chi-restraints excluded: chain M residue 399 GLU Chi-restraints excluded: chain S residue 46 THR Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 149 optimal weight: 0.0170 chunk 169 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.108276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076306 restraints weight = 28587.051| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.42 r_work: 0.3019 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16772 Z= 0.118 Angle : 0.617 15.560 22686 Z= 0.302 Chirality : 0.043 0.158 2621 Planarity : 0.004 0.044 2870 Dihedral : 8.913 171.869 2274 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.73 % Allowed : 28.42 % Favored : 68.85 % 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: 0.47 (0.19), residues: 2031 helix: 1.04 (0.16), residues: 1109 sheet: -0.32 (0.31), residues: 262 loop : -0.51 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 304 TYR 0.030 0.001 TYR H 58 PHE 0.011 0.001 PHE G 117 TRP 0.013 0.001 TRP C 172 HIS 0.010 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00270 (16767) covalent geometry : angle 0.61732 (22686) hydrogen bonds : bond 0.03383 ( 864) hydrogen bonds : angle 4.26436 ( 2616) Misc. bond : bond 0.00157 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8790.31 seconds wall clock time: 149 minutes 32.63 seconds (8972.63 seconds total)