Starting phenix.real_space_refine on Sat Jun 14 21:06:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r4h_14312/06_2025/7r4h_14312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r4h_14312/06_2025/7r4h_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_14312/06_2025/7r4h_14312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r4h_14312/06_2025/7r4h_14312.map" model { file = "/net/cci-nas-00/data/ceres_data/7r4h_14312/06_2025/7r4h_14312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r4h_14312/06_2025/7r4h_14312.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.62, per 1000 atoms: 0.58 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: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.68 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: 5.76 Time building geometry restraints manager: 4.83 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.040 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.150 ------------------------------------------------------------------------------- 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 : 5.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.003 TRP C 172 HIS 0.008 0.001 HIS G 340 PHE 0.018 0.003 PHE S 4 TYR 0.042 0.002 TYR H 58 ARG 0.027 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.13003 ( 864) hydrogen bonds : angle 7.25673 ( 2616) covalent geometry : bond 0.00616 (16767) covalent geometry : angle 1.22311 (22686) 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 : 2.120 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: 1.2335 time to fit residues: 344.1959 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 : 1.953 ------------------------------------------------------------------------------- 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 170 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN 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 = 0.3760 r_free = 0.3760 target = 0.111060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078533 restraints weight = 28919.832| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.48 r_work: 0.3082 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16772 Z= 0.148 Angle : 0.628 11.582 22686 Z= 0.320 Chirality : 0.043 0.189 2621 Planarity : 0.005 0.051 2870 Dihedral : 9.920 169.930 2342 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.14 % Allowed : 27.32 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2031 helix: -0.52 (0.14), residues: 1104 sheet: -0.58 (0.31), residues: 260 loop : -1.15 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 172 HIS 0.004 0.001 HIS S 3 PHE 0.015 0.001 PHE S 67 TYR 0.026 0.002 TYR H 58 ARG 0.007 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 864) hydrogen bonds : angle 4.82427 ( 2616) covalent geometry : bond 0.00334 (16767) covalent geometry : angle 0.62829 (22686) Misc. bond : bond 0.00166 ( 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 270 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 176 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7750 (tptp) cc_final: 0.7379 (tptp) REVERT: B 469 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6338 (t80) REVERT: C 55 THR cc_start: 0.8853 (m) cc_final: 0.8584 (t) REVERT: C 108 MET cc_start: 0.7147 (mmt) cc_final: 0.6851 (mmm) REVERT: G 228 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7895 (mpt) REVERT: G 546 LYS cc_start: 0.7990 (pptt) cc_final: 0.7756 (pptt) REVERT: H 58 TYR cc_start: 0.7945 (t80) cc_final: 0.7653 (t80) REVERT: H 86 GLN cc_start: 0.9026 (mt0) cc_final: 0.8814 (mt0) REVERT: H 105 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7946 (mm-30) REVERT: L 359 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: L 365 ILE cc_start: 0.7343 (pp) cc_final: 0.6990 (mt) REVERT: M 345 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8156 (t) REVERT: S 25 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8221 (t0) outliers start: 94 outliers final: 38 residues processed: 252 average time/residue: 1.3102 time to fit residues: 366.6146 Evaluate side-chains 203 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 197 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 C residue 48 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 92 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 68 LEU Chi-restraints excluded: chain G residue 160 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 228 MET 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 53 VAL 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 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 186 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 119 optimal weight: 0.0000 chunk 100 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077936 restraints weight = 28755.337| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.48 r_work: 0.3073 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16772 Z= 0.122 Angle : 0.594 16.478 22686 Z= 0.296 Chirality : 0.042 0.160 2621 Planarity : 0.004 0.046 2870 Dihedral : 9.215 171.374 2287 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.25 % Allowed : 26.07 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2031 helix: 0.22 (0.15), residues: 1110 sheet: -0.44 (0.31), residues: 260 loop : -0.93 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 PHE 0.012 0.001 PHE G 117 TYR 0.016 0.001 TYR H 58 ARG 0.005 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 864) hydrogen bonds : angle 4.52701 ( 2616) covalent geometry : bond 0.00273 (16767) covalent geometry : angle 0.59409 (22686) Misc. bond : bond 0.00171 ( 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 276 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 180 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.7927 (tptp) cc_final: 0.7702 (tptp) REVERT: B 91 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 469 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6248 (t80) REVERT: B 567 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (mt) REVERT: C 55 THR cc_start: 0.8898 (m) cc_final: 0.8621 (t) REVERT: C 108 MET cc_start: 0.7138 (mmt) cc_final: 0.6862 (mmm) REVERT: G 381 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6981 (mpt) REVERT: G 546 LYS cc_start: 0.7914 (pptt) cc_final: 0.7625 (pptt) REVERT: H 86 GLN cc_start: 0.9019 (mt0) cc_final: 0.8806 (mt0) REVERT: H 104 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7267 (ttp-110) REVERT: H 105 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7655 (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: 0.6765 (mp0) REVERT: L 365 ILE cc_start: 0.7257 (pp) cc_final: 0.6901 (mt) REVERT: M 177 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: M 209 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: M 345 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8207 (t) REVERT: M 378 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8451 (t) REVERT: S 25 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8245 (t0) REVERT: S 45 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7909 (pmm150) outliers start: 96 outliers final: 38 residues processed: 253 average time/residue: 1.3056 time to fit residues: 367.3951 Evaluate side-chains 213 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 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 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 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 158 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 147 optimal weight: 0.5980 chunk 160 optimal weight: 0.0570 chunk 135 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- 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 218 GLN G 340 HIS H 152 ASN M 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.109113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076496 restraints weight = 28729.660| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.48 r_work: 0.3044 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16772 Z= 0.139 Angle : 0.596 14.413 22686 Z= 0.297 Chirality : 0.043 0.170 2621 Planarity : 0.004 0.043 2870 Dihedral : 9.145 169.769 2281 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.63 % Allowed : 25.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 2031 helix: 0.63 (0.16), residues: 1099 sheet: -0.34 (0.32), residues: 257 loop : -0.76 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 172 HIS 0.005 0.001 HIS S 3 PHE 0.013 0.001 PHE G 117 TYR 0.014 0.001 TYR G 290 ARG 0.006 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 864) hydrogen bonds : angle 4.40118 ( 2616) covalent geometry : bond 0.00317 (16767) covalent geometry : angle 0.59634 (22686) Misc. bond : bond 0.00184 ( 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 275 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 172 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8049 (tptp) cc_final: 0.7793 (tptp) REVERT: B 60 THR cc_start: 0.8641 (p) cc_final: 0.8198 (t) REVERT: B 186 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: B 469 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 567 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8480 (mt) REVERT: C 55 THR cc_start: 0.8924 (m) cc_final: 0.8634 (t) REVERT: C 108 MET cc_start: 0.7233 (mmt) cc_final: 0.6948 (mmm) REVERT: G 133 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7773 (mp0) REVERT: G 209 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6442 (mm) REVERT: G 379 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8250 (mtp85) REVERT: G 381 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7175 (mpt) REVERT: G 450 GLU cc_start: 0.7864 (pm20) cc_final: 0.7578 (pm20) REVERT: G 546 LYS cc_start: 0.7941 (pptt) cc_final: 0.7656 (pptt) REVERT: H 58 TYR cc_start: 0.8312 (t80) cc_final: 0.8057 (t80) REVERT: H 86 GLN cc_start: 0.9085 (mt0) cc_final: 0.8861 (mt0) REVERT: H 104 ARG cc_start: 0.7879 (ttt90) cc_final: 0.7254 (ttp-110) REVERT: H 105 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7664 (mm-30) REVERT: H 130 LEU cc_start: 0.7667 (pt) cc_final: 0.7443 (pp) REVERT: L 359 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: L 365 ILE cc_start: 0.7204 (pp) cc_final: 0.6885 (mt) REVERT: M 177 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: M 209 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: S 25 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8260 (t0) REVERT: S 26 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8906 (mppt) outliers start: 103 outliers final: 47 residues processed: 253 average time/residue: 1.3998 time to fit residues: 394.6906 Evaluate side-chains 222 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 1.925 ------------------------------------------------------------------------------- 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 186 GLU Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 257 LEU 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 440 ASP Chi-restraints excluded: chain B residue 469 PHE 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 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 209 LEU Chi-restraints excluded: chain G residue 240 ILE 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 372 LEU 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 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 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 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 25 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 172 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS S 3 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.109235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076611 restraints weight = 29118.978| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.50 r_work: 0.3044 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16772 Z= 0.125 Angle : 0.583 13.688 22686 Z= 0.289 Chirality : 0.043 0.225 2621 Planarity : 0.004 0.043 2870 Dihedral : 9.079 170.555 2279 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.97 % Allowed : 25.52 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2031 helix: 0.77 (0.16), residues: 1109 sheet: -0.42 (0.32), residues: 258 loop : -0.71 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 172 HIS 0.005 0.001 HIS G 235 PHE 0.012 0.001 PHE G 117 TYR 0.013 0.001 TYR M 134 ARG 0.004 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 864) hydrogen bonds : angle 4.32265 ( 2616) covalent geometry : bond 0.00284 (16767) covalent geometry : angle 0.58251 (22686) Misc. bond : bond 0.00169 ( 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 262 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 171 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8112 (tptp) cc_final: 0.7826 (tptp) REVERT: B 60 THR cc_start: 0.8662 (p) cc_final: 0.8211 (t) REVERT: B 469 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6795 (t80) REVERT: C 55 THR cc_start: 0.8929 (m) cc_final: 0.8627 (t) REVERT: C 108 MET cc_start: 0.7361 (mmt) cc_final: 0.7076 (mmm) REVERT: C 110 MET cc_start: 0.8131 (tmm) cc_final: 0.7927 (tmt) REVERT: G 133 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7842 (mp0) REVERT: G 300 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8070 (ptmm) REVERT: G 379 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8267 (mtp85) REVERT: G 450 GLU cc_start: 0.7821 (pm20) cc_final: 0.7527 (pm20) REVERT: G 546 LYS cc_start: 0.7950 (pptt) cc_final: 0.7629 (pptt) REVERT: H 58 TYR cc_start: 0.8405 (t80) cc_final: 0.8080 (t80) REVERT: H 86 GLN cc_start: 0.9080 (mt0) cc_final: 0.8850 (mt0) REVERT: H 104 ARG cc_start: 0.7883 (ttt90) cc_final: 0.7330 (ttp-110) REVERT: H 105 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7667 (mm-30) REVERT: L 359 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: L 360 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: L 365 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6883 (mt) REVERT: M 177 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: M 209 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: M 378 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8456 (t) REVERT: S 25 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (t0) REVERT: S 26 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8902 (mppt) outliers start: 91 outliers final: 42 residues processed: 240 average time/residue: 1.3167 time to fit residues: 350.9458 Evaluate side-chains 219 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 PHE 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 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 240 ILE 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 L residue 359 GLN Chi-restraints excluded: chain L residue 360 GLU Chi-restraints excluded: chain L residue 365 ILE 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 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 25 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 184 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073336 restraints weight = 28835.069| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.45 r_work: 0.2977 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16772 Z= 0.199 Angle : 0.630 12.824 22686 Z= 0.314 Chirality : 0.045 0.185 2621 Planarity : 0.004 0.044 2870 Dihedral : 9.311 167.051 2278 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.08 % Allowed : 25.08 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2031 helix: 0.79 (0.16), residues: 1107 sheet: -0.41 (0.32), residues: 263 loop : -0.68 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 172 HIS 0.005 0.001 HIS H 80 PHE 0.015 0.002 PHE G 117 TYR 0.017 0.002 TYR G 290 ARG 0.008 0.001 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 864) hydrogen bonds : angle 4.42378 ( 2616) covalent geometry : bond 0.00467 (16767) covalent geometry : angle 0.63033 (22686) Misc. bond : bond 0.00206 ( 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 257 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 164 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8192 (tptp) cc_final: 0.7852 (tptp) REVERT: B 60 THR cc_start: 0.8686 (p) cc_final: 0.8306 (t) REVERT: B 439 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4973 (pp) REVERT: B 460 ASP cc_start: 0.8041 (m-30) cc_final: 0.7380 (p0) REVERT: B 469 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7249 (t80) REVERT: B 476 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6615 (ptpp) REVERT: C 55 THR cc_start: 0.8986 (m) cc_final: 0.8703 (t) REVERT: C 108 MET cc_start: 0.7601 (mmt) cc_final: 0.7319 (mmm) REVERT: C 176 GLN cc_start: 0.7850 (pm20) cc_final: 0.7404 (pm20) REVERT: G 56 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8348 (mtt) REVERT: G 133 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7819 (mp0) REVERT: G 180 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8130 (mmpt) REVERT: G 450 GLU cc_start: 0.7810 (pm20) cc_final: 0.7453 (pm20) REVERT: G 546 LYS cc_start: 0.8003 (pptt) cc_final: 0.7685 (pptt) REVERT: H 86 GLN cc_start: 0.9146 (mt0) cc_final: 0.8923 (mt0) REVERT: H 104 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7407 (ttp-110) REVERT: H 105 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7843 (mm-30) REVERT: L 359 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: L 365 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6931 (mt) REVERT: M 41 GLU cc_start: 0.8582 (tt0) cc_final: 0.8090 (tm-30) REVERT: M 177 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: M 209 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: S 10 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8124 (mtt90) REVERT: S 26 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8987 (mppt) outliers start: 93 outliers final: 44 residues processed: 240 average time/residue: 1.2610 time to fit residues: 337.6857 Evaluate side-chains 212 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP 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 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 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 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 164 ILE 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 345 VAL Chi-restraints excluded: chain M residue 378 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 60 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN C 126 ASN C 132 ASN C 176 GLN G 340 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.107406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074760 restraints weight = 28708.781| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.45 r_work: 0.3006 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2313 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= 0.135 Angle : 0.592 12.838 22686 Z= 0.295 Chirality : 0.043 0.224 2621 Planarity : 0.004 0.044 2870 Dihedral : 9.178 169.779 2276 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.43 % Allowed : 26.12 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2031 helix: 0.88 (0.16), residues: 1108 sheet: -0.34 (0.32), residues: 258 loop : -0.65 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 172 HIS 0.006 0.001 HIS G 100 PHE 0.012 0.001 PHE G 117 TYR 0.014 0.001 TYR H 58 ARG 0.004 0.000 ARG M 167 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 864) hydrogen bonds : angle 4.32743 ( 2616) covalent geometry : bond 0.00313 (16767) covalent geometry : angle 0.59234 (22686) Misc. bond : bond 0.00166 ( 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 246 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8221 (tptp) cc_final: 0.7954 (tptp) REVERT: B 60 THR cc_start: 0.8673 (p) cc_final: 0.8291 (t) REVERT: B 439 LEU cc_start: 0.5202 (OUTLIER) cc_final: 0.4861 (pp) REVERT: B 460 ASP cc_start: 0.8001 (m-30) cc_final: 0.7380 (p0) REVERT: B 476 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6488 (ptpp) REVERT: C 108 MET cc_start: 0.7613 (mmt) cc_final: 0.7331 (mmm) REVERT: G 133 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7818 (mp0) REVERT: G 209 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6490 (mm) REVERT: G 379 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8206 (mtp85) REVERT: G 381 MET cc_start: 0.7394 (mpt) cc_final: 0.6918 (mpt) REVERT: G 450 GLU cc_start: 0.7810 (pm20) cc_final: 0.7418 (pm20) REVERT: G 546 LYS cc_start: 0.8012 (pptt) cc_final: 0.7680 (pptt) REVERT: H 86 GLN cc_start: 0.9090 (mt0) cc_final: 0.8807 (mt0) REVERT: H 104 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7402 (ttp-110) REVERT: H 105 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7871 (mm-30) REVERT: L 359 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: L 365 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6800 (mt) REVERT: M 41 GLU cc_start: 0.8606 (tt0) cc_final: 0.8147 (tm-30) REVERT: M 177 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: M 209 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: S 25 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (t0) outliers start: 81 outliers final: 46 residues processed: 232 average time/residue: 1.3539 time to fit residues: 349.0488 Evaluate side-chains 213 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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 323 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 ASP 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 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 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 68 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 240 ILE Chi-restraints excluded: chain G residue 284 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 H residue 175 ASN 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 164 ILE 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 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 107 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 126 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 = 0.3676 r_free = 0.3676 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073221 restraints weight = 28844.460| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.42 r_work: 0.2954 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16772 Z= 0.209 Angle : 0.652 13.789 22686 Z= 0.326 Chirality : 0.046 0.205 2621 Planarity : 0.004 0.045 2870 Dihedral : 9.409 167.463 2276 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.37 % Allowed : 26.12 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2031 helix: 0.87 (0.16), residues: 1100 sheet: -0.49 (0.31), residues: 265 loop : -0.63 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 172 HIS 0.008 0.001 HIS G 100 PHE 0.015 0.002 PHE G 117 TYR 0.018 0.002 TYR G 290 ARG 0.009 0.001 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 864) hydrogen bonds : angle 4.46413 ( 2616) covalent geometry : bond 0.00495 (16767) covalent geometry : angle 0.65231 (22686) Misc. bond : bond 0.00205 ( 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 237 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 157 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8225 (tptp) cc_final: 0.7946 (tptp) REVERT: B 60 THR cc_start: 0.8722 (p) cc_final: 0.8423 (t) REVERT: B 122 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (pp) REVERT: B 439 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.5086 (pp) REVERT: B 460 ASP cc_start: 0.8129 (m-30) cc_final: 0.7579 (p0) REVERT: B 476 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6569 (ptpp) REVERT: B 498 GLU cc_start: 0.8419 (pm20) cc_final: 0.8052 (pm20) REVERT: C 108 MET cc_start: 0.7701 (mmt) cc_final: 0.7434 (mmm) REVERT: G 56 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8430 (mtt) REVERT: G 133 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7913 (mp0) REVERT: G 209 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6942 (mm) REVERT: G 340 HIS cc_start: 0.8402 (t70) cc_final: 0.8198 (t-90) REVERT: G 379 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8074 (mtp85) REVERT: G 381 MET cc_start: 0.7247 (mpt) cc_final: 0.6951 (mpt) REVERT: G 450 GLU cc_start: 0.7842 (pm20) cc_final: 0.7505 (pm20) REVERT: G 546 LYS cc_start: 0.8019 (pptt) cc_final: 0.7609 (pptt) REVERT: H 83 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8337 (mt0) REVERT: H 105 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7999 (mm-30) REVERT: L 359 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: M 41 GLU cc_start: 0.8653 (tt0) cc_final: 0.8174 (tm-30) REVERT: M 130 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8412 (pp) REVERT: M 177 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: M 209 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: S 10 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8209 (mtt90) outliers start: 80 outliers final: 48 residues processed: 222 average time/residue: 1.5379 time to fit residues: 380.3371 Evaluate side-chains 209 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 122 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 267 MET 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 440 ASP Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 476 LYS 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 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 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 209 LEU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 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 83 GLN 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 130 ILE Chi-restraints excluded: chain M residue 164 ILE 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 345 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 387 THR 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 61 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN G 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.107497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075495 restraints weight = 28576.013| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.42 r_work: 0.3003 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16772 Z= 0.123 Angle : 0.608 12.884 22686 Z= 0.301 Chirality : 0.043 0.192 2621 Planarity : 0.004 0.044 2870 Dihedral : 9.168 170.324 2276 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.44 % Allowed : 27.05 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2031 helix: 0.96 (0.16), residues: 1108 sheet: -0.43 (0.31), residues: 256 loop : -0.61 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 172 HIS 0.004 0.001 HIS G 235 PHE 0.011 0.001 PHE G 117 TYR 0.026 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 864) hydrogen bonds : angle 4.31656 ( 2616) covalent geometry : bond 0.00282 (16767) covalent geometry : angle 0.60801 (22686) Misc. bond : bond 0.00160 ( 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 217 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8285 (tptp) cc_final: 0.8011 (tptp) REVERT: B 60 THR cc_start: 0.8593 (p) cc_final: 0.8268 (t) REVERT: B 460 ASP cc_start: 0.8146 (m-30) cc_final: 0.7574 (p0) REVERT: B 498 GLU cc_start: 0.8413 (pm20) cc_final: 0.8034 (pm20) REVERT: C 108 MET cc_start: 0.7719 (mmt) cc_final: 0.7450 (mmm) REVERT: G 101 LEU cc_start: 0.8902 (tm) cc_final: 0.8681 (tt) REVERT: G 133 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7802 (mp0) REVERT: G 209 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6472 (mm) REVERT: G 379 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8138 (mtp85) REVERT: G 381 MET cc_start: 0.7232 (mpt) cc_final: 0.6960 (mpt) REVERT: G 546 LYS cc_start: 0.7939 (pptt) cc_final: 0.7672 (pptt) REVERT: H 105 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7951 (mm-30) REVERT: L 359 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: M 41 GLU cc_start: 0.8566 (tt0) cc_final: 0.8092 (tm-30) REVERT: M 337 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: S 25 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8267 (t0) outliers start: 63 outliers final: 44 residues processed: 206 average time/residue: 1.5395 time to fit residues: 352.0455 Evaluate side-chains 199 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 PHE 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 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 209 LEU 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 366 MET 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 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 34 MET Chi-restraints excluded: chain M residue 99 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 337 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 115 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** G 97 GLN G 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075340 restraints weight = 28702.552| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.41 r_work: 0.3001 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16772 Z= 0.134 Angle : 0.620 13.964 22686 Z= 0.306 Chirality : 0.043 0.160 2621 Planarity : 0.004 0.047 2870 Dihedral : 9.132 170.385 2276 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.01 % Allowed : 27.65 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2031 helix: 0.99 (0.16), residues: 1108 sheet: -0.47 (0.31), residues: 259 loop : -0.57 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 172 HIS 0.007 0.001 HIS G 100 PHE 0.026 0.001 PHE B 91 TYR 0.028 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 864) hydrogen bonds : angle 4.31436 ( 2616) covalent geometry : bond 0.00311 (16767) covalent geometry : angle 0.61997 (22686) Misc. bond : bond 0.00173 ( 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 209 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8273 (tptp) cc_final: 0.7988 (tptp) REVERT: B 60 THR cc_start: 0.8607 (p) cc_final: 0.8294 (t) REVERT: B 460 ASP cc_start: 0.8146 (m-30) cc_final: 0.7581 (p0) REVERT: B 498 GLU cc_start: 0.8409 (pm20) cc_final: 0.8031 (pm20) REVERT: C 108 MET cc_start: 0.7777 (mmt) cc_final: 0.7503 (mmm) REVERT: G 101 LEU cc_start: 0.8866 (tm) cc_final: 0.8662 (tt) REVERT: G 133 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7832 (mp0) REVERT: G 209 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6457 (mm) REVERT: G 340 HIS cc_start: 0.8489 (t70) cc_final: 0.8289 (t-90) REVERT: G 379 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: G 381 MET cc_start: 0.7228 (mpt) cc_final: 0.6945 (mpt) REVERT: G 416 ARG cc_start: 0.8021 (tmt170) cc_final: 0.7662 (tmt170) REVERT: G 546 LYS cc_start: 0.7943 (pptt) cc_final: 0.7674 (pptt) REVERT: H 105 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7953 (mm-30) REVERT: L 359 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: M 41 GLU cc_start: 0.8564 (tt0) cc_final: 0.8090 (tm-30) REVERT: S 25 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8310 (t0) outliers start: 55 outliers final: 46 residues processed: 199 average time/residue: 1.3580 time to fit residues: 299.9204 Evaluate side-chains 201 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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 267 MET Chi-restraints excluded: chain B residue 323 VAL 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 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 140 THR 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 209 LEU Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 366 MET 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 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 30 VAL Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 99 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 145 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.107532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075600 restraints weight = 28761.548| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.43 r_work: 0.3004 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16772 Z= 0.129 Angle : 0.621 14.307 22686 Z= 0.305 Chirality : 0.043 0.178 2621 Planarity : 0.004 0.047 2870 Dihedral : 9.075 170.779 2276 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.11 % Allowed : 27.49 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2031 helix: 1.02 (0.16), residues: 1110 sheet: -0.44 (0.31), residues: 259 loop : -0.51 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 172 HIS 0.007 0.001 HIS G 100 PHE 0.012 0.001 PHE G 117 TYR 0.025 0.001 TYR H 58 ARG 0.009 0.000 ARG M 304 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 864) hydrogen bonds : angle 4.29603 ( 2616) covalent geometry : bond 0.00299 (16767) covalent geometry : angle 0.62054 (22686) Misc. bond : bond 0.00169 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19760.61 seconds wall clock time: 342 minutes 38.55 seconds (20558.55 seconds total)