Starting phenix.real_space_refine on Mon Jul 6 13:57:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gft_29984/07_2026/8gft_29984.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 Mn 2 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 11253 2.51 5 N 3013 2.21 5 O 3426 1.98 5 H 17686 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35483 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 10411 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 17, 'TRANS': 621} Chain breaks: 1 Chain: "B" Number of atoms: 10284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 10284 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "C" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4307 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain: "D" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3101 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 7316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7316 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 16, 'TRANS': 442} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 5.70, per 1000 atoms: 0.16 Number of scatterers: 35483 At special positions: 0 Unit cell: (149.465, 156.145, 156.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 2 24.99 K 2 19.00 S 93 16.00 P 6 15.00 Mg 2 11.99 O 3426 8.00 N 3013 7.00 C 11253 6.00 H 17686 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 920.0 milliseconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 52.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 4.064A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 59 removed outlier: 4.308A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.545A pdb=" N ALA A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.794A pdb=" N TYR A 192 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 398 through 420 Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.031A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.673A pdb=" N CYS A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.605A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.545A pdb=" N GLY A 618 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 619 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 621 " --> pdb=" O GLY A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 4.077A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.659A pdb=" N ARG B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 61 No H-bonds generated for 'chain 'B' and resid 60 through 61' Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.810A pdb=" N LEU B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.555A pdb=" N ALA B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 removed outlier: 3.506A pdb=" N TYR B 135 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.966A pdb=" N THR B 191 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 192 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 193 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 398 through 420 removed outlier: 3.644A pdb=" N LYS B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 6.297A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 4.155A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 517 through 525 removed outlier: 4.190A pdb=" N GLN B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.341A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 575 removed outlier: 4.051A pdb=" N VAL B 575 " --> pdb=" O ASP B 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 575' Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.550A pdb=" N ARG B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.849A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 24 through 73 removed outlier: 3.617A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 110 removed outlier: 5.497A pdb=" N GLU C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.550A pdb=" N GLU C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 157 through 161 removed outlier: 4.163A pdb=" N LYS C 160 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 179 through 182 Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.592A pdb=" N VAL C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 202 through 227 removed outlier: 3.682A pdb=" N HIS C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 234 through 243 removed outlier: 3.587A pdb=" N PHE C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 5.099A pdb=" N GLU C 257 " --> pdb=" O ASN C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 435 Processing helix chain 'D' and resid 441 through 462 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 526 through 542 Processing helix chain 'D' and resid 553 through 563 Processing helix chain 'D' and resid 569 through 573 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.851A pdb=" N GLU E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 Processing helix chain 'E' and resid 61 through 75 removed outlier: 3.967A pdb=" N TYR E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 92 Processing helix chain 'E' and resid 95 through 109 Processing helix chain 'E' and resid 111 through 126 Processing helix chain 'E' and resid 131 through 153 removed outlier: 4.620A pdb=" N LYS E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.558A pdb=" N MET E 170 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 Processing helix chain 'E' and resid 205 through 221 Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 278 through 293 removed outlier: 3.653A pdb=" N LEU E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.718A pdb=" N TRP E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 368 Processing helix chain 'E' and resid 379 through 387 Processing helix chain 'E' and resid 407 through 419 removed outlier: 4.509A pdb=" N THR E 411 " --> pdb=" O GLY E 407 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 413 " --> pdb=" O ASP E 409 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 417 " --> pdb=" O ALA E 413 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN E 418 " --> pdb=" O PHE E 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.894A pdb=" N HIS B 185 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 144 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 183 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 146 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS B 181 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 148 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY B 179 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 84 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.991A pdb=" N GLN A 18 " --> pdb=" O ILE B 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.893A pdb=" N ILE A 277 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 215 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.688A pdb=" N ILE A 335 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 318 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 333 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS A 320 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 331 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE A 329 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468 removed outlier: 4.461A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL A 511 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR A 484 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET A 513 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 486 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580 removed outlier: 6.598A pdb=" N LYS A 577 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 628 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 579 " --> pdb=" O ILE A 628 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 360 through 363 removed outlier: 7.055A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 329 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER B 322 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 331 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS B 320 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 333 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 318 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 335 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LEU B 316 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 129 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 318 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER C 127 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N HIS B 320 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER C 125 " --> pdb=" O HIS B 320 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER B 322 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 458 through 459 removed outlier: 4.412A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL B 511 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR B 484 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N MET B 513 " --> pdb=" O TYR B 484 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE B 486 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580 removed outlier: 6.495A pdb=" N LYS B 577 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B 628 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 579 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 474 through 476 Processing sheet with id=AB4, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.607A pdb=" N VAL E 227 " --> pdb=" O CYS E 343 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 349 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 298 through 299 removed outlier: 5.905A pdb=" N GLN E 465 " --> pdb=" O ARG E 470 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ARG E 470 " --> pdb=" O GLN E 465 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2397 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: 8.95 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.52 - 0.79: 3 0.79 - 1.06: 4082 1.06 - 1.32: 17496 1.32 - 1.59: 14056 1.59 - 1.86: 165 Bond restraints: 35802 Sorted by residual: bond pdb=" N SEP C 13 " pdb=" H SEP C 13 " ideal model delta sigma weight residual 0.860 0.523 0.337 2.00e-02 2.50e+03 2.84e+02 bond pdb=" CB SER B 490 " pdb=" OG SER B 490 " ideal model delta sigma weight residual 1.417 1.099 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" CE1 HIS E 205 " pdb=" NE2 HIS E 205 " ideal model delta sigma weight residual 1.321 1.193 0.128 1.00e-02 1.00e+04 1.65e+02 bond pdb=" CZ ARG B 612 " pdb=" NH2 ARG B 612 " ideal model delta sigma weight residual 1.330 1.177 0.153 1.30e-02 5.92e+03 1.39e+02 bond pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta sigma weight residual 1.446 1.323 0.123 1.26e-02 6.30e+03 9.51e+01 ... (remaining 35797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.47: 64225 7.47 - 14.93: 534 14.93 - 22.40: 19 22.40 - 29.87: 6 29.87 - 37.33: 5 Bond angle restraints: 64789 Sorted by residual: angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 123.03 16.84 1.00e+00 1.00e+00 2.84e+02 angle pdb=" CA VAL E 402 " pdb=" CB VAL E 402 " pdb=" CG1 VAL E 402 " ideal model delta sigma weight residual 110.40 138.06 -27.66 1.70e+00 3.46e-01 2.65e+02 angle pdb=" PA ATP B 802 " pdb=" O3A ATP B 802 " pdb=" PB ATP B 802 " ideal model delta sigma weight residual 136.83 121.37 15.46 1.00e+00 1.00e+00 2.39e+02 angle pdb=" N TYR B 212 " pdb=" CA TYR B 212 " pdb=" HA TYR B 212 " ideal model delta sigma weight residual 110.00 72.67 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" C LYS B 435 " pdb=" N ASN B 436 " pdb=" CA ASN B 436 " ideal model delta sigma weight residual 120.65 136.98 -16.33 1.32e+00 5.74e-01 1.53e+02 ... (remaining 64784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.22: 16212 30.22 - 60.44: 428 60.44 - 90.66: 57 90.66 - 120.87: 2 120.87 - 151.09: 1 Dihedral angle restraints: 16700 sinusoidal: 9209 harmonic: 7491 Sorted by residual: dihedral pdb=" C CYS E 382 " pdb=" N CYS E 382 " pdb=" CA CYS E 382 " pdb=" CB CYS E 382 " ideal model delta harmonic sigma weight residual -122.60 -141.56 18.96 0 2.50e+00 1.60e-01 5.75e+01 dihedral pdb=" N CYS E 382 " pdb=" C CYS E 382 " pdb=" CA CYS E 382 " pdb=" CB CYS E 382 " ideal model delta harmonic sigma weight residual 122.80 140.73 -17.93 0 2.50e+00 1.60e-01 5.14e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 91.09 -151.09 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 16697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2592 0.287 - 0.575: 53 0.575 - 0.862: 5 0.862 - 1.149: 1 1.149 - 1.437: 1 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB VAL E 402 " pdb=" CA VAL E 402 " pdb=" CG1 VAL E 402 " pdb=" CG2 VAL E 402 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.16e+01 chirality pdb=" CA CYS E 382 " pdb=" N CYS E 382 " pdb=" C CYS E 382 " pdb=" CB CYS E 382 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA ASP E 155 " pdb=" N ASP E 155 " pdb=" C ASP E 155 " pdb=" CB ASP E 155 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 2649 not shown) Planarity restraints: 5239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 446 " -0.359 2.00e-02 2.50e+03 1.37e-01 5.62e+02 pdb=" CG PHE E 446 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE E 446 " 0.119 2.00e-02 2.50e+03 pdb=" CD2 PHE E 446 " 0.133 2.00e-02 2.50e+03 pdb=" CE1 PHE E 446 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE E 446 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE E 446 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE E 446 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE E 446 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE E 446 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE E 446 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE E 446 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 596 " 0.180 2.00e-02 2.50e+03 1.19e-01 4.27e+02 pdb=" CG TYR A 596 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 596 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 596 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 596 " -0.142 2.00e-02 2.50e+03 pdb=" CE2 TYR A 596 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 596 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 596 " 0.160 2.00e-02 2.50e+03 pdb=" HD1 TYR A 596 " 0.150 2.00e-02 2.50e+03 pdb=" HD2 TYR A 596 " -0.155 2.00e-02 2.50e+03 pdb=" HE1 TYR A 596 " -0.127 2.00e-02 2.50e+03 pdb=" HE2 TYR A 596 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 619 " 0.241 2.00e-02 2.50e+03 9.96e-02 2.98e+02 pdb=" CG TYR A 619 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 619 " -0.100 2.00e-02 2.50e+03 pdb=" CD2 TYR A 619 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 619 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 619 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 619 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 619 " 0.172 2.00e-02 2.50e+03 pdb=" HD1 TYR A 619 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 TYR A 619 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 619 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 619 " -0.061 2.00e-02 2.50e+03 ... (remaining 5236 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.35: 6288 2.35 - 3.05: 102365 3.05 - 3.75: 125821 3.75 - 4.44: 191218 4.44 - 5.14: 294567 Nonbonded interactions: 720259 Sorted by model distance: nonbonded pdb=" OD1 ASP E 307 " pdb=" HH TYR E 328 " model vdw 1.655 2.450 nonbonded pdb=" HG SER B 68 " pdb=" OD1 ASN B 151 " model vdw 1.655 2.450 nonbonded pdb=" OD1 ASP B 444 " pdb=" HG1 THR B 446 " model vdw 1.660 2.450 nonbonded pdb=" HG SER A 581 " pdb=" OE1 GLU A 627 " model vdw 1.660 2.450 nonbonded pdb=" HH TYR E 422 " pdb=" O LEU E 469 " model vdw 1.660 2.450 ... (remaining 720254 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 'A' and (resid 10 through 220 or resid 273 through 691 or resid 803)) selection = (chain 'B' and (resid 11 through 691 or resid 803)) } 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 group one per residue 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: 2.130 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: 0.220 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.020 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.017 0.318 18116 Z= 0.993 Angle : 1.959 27.660 24370 Z= 1.329 Chirality : 0.119 1.437 2652 Planarity : 0.016 0.217 3127 Dihedral : 13.211 151.092 6995 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2162 helix: -0.78 (0.14), residues: 959 sheet: 0.33 (0.32), residues: 256 loop : -0.24 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG B 449 TYR 0.215 0.021 TYR A 619 PHE 0.236 0.013 PHE E 446 TRP 0.121 0.022 TRP C 114 HIS 0.012 0.003 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.01694 / 0.99 (18116) covalent geometry : angle 1.95882 / 1.33 (24370) hydrogen bonds : bond 0.18140 / 12.07 ( 861) hydrogen bonds : angle 7.35360 / 5.09 ( 2397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.9059 (ttt) cc_final: 0.8855 (tpp) REVERT: A 606 MET cc_start: 0.9570 (mmp) cc_final: 0.9327 (mmp) REVERT: C 216 MET cc_start: 0.9383 (mmm) cc_final: 0.9002 (tpp) REVERT: D 553 ASN cc_start: 0.9250 (t0) cc_final: 0.8580 (t0) REVERT: D 555 ASP cc_start: 0.8918 (m-30) cc_final: 0.8499 (p0) REVERT: E 141 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8985 (tptp) REVERT: E 170 MET cc_start: 0.8427 (mmp) cc_final: 0.8124 (mpp) REVERT: E 213 LEU cc_start: 0.9126 (mt) cc_final: 0.8923 (mt) REVERT: E 327 MET cc_start: 0.9465 (tpt) cc_final: 0.8930 (mmt) REVERT: E 331 PHE cc_start: 0.9465 (m-80) cc_final: 0.9204 (t80) REVERT: E 332 SER cc_start: 0.9461 (t) cc_final: 0.9203 (p) REVERT: E 333 GLU cc_start: 0.9268 (tp30) cc_final: 0.9022 (tp30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3578 time to fit residues: 79.5085 Evaluate side-chains 111 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 207 GLN B 150 HIS C 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.060560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.043239 restraints weight = 415302.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044563 restraints weight = 185090.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.044547 restraints weight = 98575.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044661 restraints weight = 90343.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044645 restraints weight = 84778.218| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18116 Z= 0.213 Angle : 0.693 9.190 24370 Z= 0.385 Chirality : 0.049 1.285 2652 Planarity : 0.004 0.049 3127 Dihedral : 8.077 115.741 2416 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.41 % Allowed : 3.17 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2162 helix: 0.39 (0.16), residues: 983 sheet: -0.31 (0.31), residues: 264 loop : -0.51 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 36 TYR 0.019 0.002 TYR E 328 PHE 0.026 0.002 PHE E 190 TRP 0.014 0.001 TRP C 193 HIS 0.009 0.002 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (18116) covalent geometry : angle 0.69259 / 0.38 (24370) hydrogen bonds : bond 0.05596 / 3.75 ( 861) hydrogen bonds : angle 5.46455 / 3.74 ( 2397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.9582 (mmp) cc_final: 0.9362 (mmm) REVERT: B 567 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8924 (mtp) REVERT: C 216 MET cc_start: 0.9536 (mmm) cc_final: 0.9074 (tpp) REVERT: E 170 MET cc_start: 0.8494 (mmp) cc_final: 0.8238 (mpp) REVERT: E 309 MET cc_start: 0.6317 (mmt) cc_final: 0.5750 (tmm) REVERT: E 333 GLU cc_start: 0.9298 (tp30) cc_final: 0.8953 (tp30) outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.3389 time to fit residues: 59.4120 Evaluate side-chains 105 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 174 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 178 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 184 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 HIS E 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.060199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042114 restraints weight = 416247.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043347 restraints weight = 174359.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043978 restraints weight = 106499.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.044349 restraints weight = 83319.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044549 restraints weight = 74107.993| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18116 Z= 0.176 Angle : 0.590 10.094 24370 Z= 0.327 Chirality : 0.048 1.380 2652 Planarity : 0.003 0.039 3127 Dihedral : 7.233 103.245 2416 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.46 % Allowed : 4.29 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2162 helix: 0.94 (0.16), residues: 981 sheet: -0.42 (0.31), residues: 265 loop : -0.58 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 395 TYR 0.013 0.001 TYR A 619 PHE 0.017 0.001 PHE E 446 TRP 0.011 0.001 TRP B 158 HIS 0.009 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (18116) covalent geometry : angle 0.59028 / 0.33 (24370) hydrogen bonds : bond 0.04627 / 3.11 ( 861) hydrogen bonds : angle 5.06660 / 3.45 ( 2397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8808 (mtp) REVERT: B 567 MET cc_start: 0.9133 (mtp) cc_final: 0.8921 (mtp) REVERT: C 216 MET cc_start: 0.9426 (mmm) cc_final: 0.9032 (tpp) REVERT: E 170 MET cc_start: 0.8570 (mmp) cc_final: 0.8333 (mpp) REVERT: E 309 MET cc_start: 0.6152 (mmt) cc_final: 0.5616 (tmm) REVERT: E 333 GLU cc_start: 0.9319 (tp30) cc_final: 0.9030 (tp30) REVERT: E 351 MET cc_start: 0.5613 (ptp) cc_final: 0.5290 (ptp) outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.3430 time to fit residues: 55.8008 Evaluate side-chains 102 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 146 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 174 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.060004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.042769 restraints weight = 415818.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.044276 restraints weight = 191366.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044160 restraints weight = 95376.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.044269 restraints weight = 82790.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.044312 restraints weight = 81143.820| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18116 Z= 0.133 Angle : 0.537 10.351 24370 Z= 0.293 Chirality : 0.048 1.450 2652 Planarity : 0.003 0.032 3127 Dihedral : 6.697 95.061 2416 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.46 % Allowed : 4.39 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2162 helix: 1.30 (0.17), residues: 984 sheet: -0.46 (0.31), residues: 272 loop : -0.58 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 467 TYR 0.010 0.001 TYR E 328 PHE 0.015 0.001 PHE E 446 TRP 0.022 0.001 TRP E 386 HIS 0.007 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (18116) covalent geometry : angle 0.53679 / 0.29 (24370) hydrogen bonds : bond 0.03931 / 2.64 ( 861) hydrogen bonds : angle 4.69766 / 3.18 ( 2397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8386 (ptm) cc_final: 0.8101 (ppp) REVERT: A 606 MET cc_start: 0.9299 (mmm) cc_final: 0.8920 (mmt) REVERT: B 126 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8781 (mtp) REVERT: B 567 MET cc_start: 0.9135 (mtp) cc_final: 0.8898 (mtp) REVERT: C 216 MET cc_start: 0.9567 (mmm) cc_final: 0.9185 (tpp) REVERT: D 456 MET cc_start: 0.9400 (mmm) cc_final: 0.9072 (mmt) REVERT: E 170 MET cc_start: 0.8430 (mmp) cc_final: 0.8186 (mpp) REVERT: E 309 MET cc_start: 0.6405 (mmt) cc_final: 0.5774 (tmm) REVERT: E 316 GLU cc_start: 0.8746 (tp30) cc_final: 0.8254 (tp30) REVERT: E 333 GLU cc_start: 0.9344 (tp30) cc_final: 0.8982 (tp30) REVERT: E 351 MET cc_start: 0.6113 (ptp) cc_final: 0.5879 (ptp) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.3343 time to fit residues: 54.6472 Evaluate side-chains 105 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 145 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 165 optimal weight: 40.0000 chunk 182 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN D 422 GLN ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.062682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.044957 restraints weight = 398184.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046819 restraints weight = 192044.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.046530 restraints weight = 101514.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.046656 restraints weight = 95454.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046726 restraints weight = 92591.819| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 18116 Z= 0.216 Angle : 0.555 10.247 24370 Z= 0.305 Chirality : 0.047 1.391 2652 Planarity : 0.003 0.074 3127 Dihedral : 6.663 107.718 2416 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.66 % Allowed : 4.96 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2162 helix: 1.36 (0.17), residues: 975 sheet: -0.68 (0.30), residues: 279 loop : -0.74 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 612 TYR 0.013 0.001 TYR A 192 PHE 0.014 0.001 PHE E 190 TRP 0.011 0.001 TRP B 158 HIS 0.008 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (18116) covalent geometry : angle 0.55480 / 0.30 (24370) hydrogen bonds : bond 0.03851 / 2.58 ( 861) hydrogen bonds : angle 4.75289 / 3.22 ( 2397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8483 (ptm) cc_final: 0.8186 (ppp) REVERT: A 567 MET cc_start: 0.9318 (mtm) cc_final: 0.8908 (mpp) REVERT: A 602 MET cc_start: 0.8994 (tpp) cc_final: 0.8701 (tpp) REVERT: A 606 MET cc_start: 0.9327 (mmm) cc_final: 0.9036 (mmt) REVERT: B 126 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8802 (mtp) REVERT: B 567 MET cc_start: 0.9109 (mtp) cc_final: 0.8755 (mtp) REVERT: C 216 MET cc_start: 0.9587 (mmm) cc_final: 0.9232 (tpp) REVERT: D 456 MET cc_start: 0.9475 (mmm) cc_final: 0.9150 (mmt) REVERT: E 309 MET cc_start: 0.6540 (mmt) cc_final: 0.5833 (tmm) REVERT: E 333 GLU cc_start: 0.9319 (tp30) cc_final: 0.8883 (tp30) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.3104 time to fit residues: 52.6628 Evaluate side-chains 109 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 474 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.063347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.045060 restraints weight = 389169.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.046884 restraints weight = 196843.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046549 restraints weight = 105326.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046901 restraints weight = 110070.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046927 restraints weight = 92210.028| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18116 Z= 0.115 Angle : 0.500 10.425 24370 Z= 0.271 Chirality : 0.047 1.425 2652 Planarity : 0.003 0.027 3127 Dihedral : 6.346 104.242 2416 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.46 % Allowed : 5.52 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2162 helix: 1.59 (0.17), residues: 989 sheet: -0.59 (0.31), residues: 272 loop : -0.68 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 66 TYR 0.009 0.001 TYR B 193 PHE 0.016 0.001 PHE E 190 TRP 0.012 0.001 TRP E 386 HIS 0.006 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18116) covalent geometry : angle 0.50015 / 0.27 (24370) hydrogen bonds : bond 0.03455 / 2.31 ( 861) hydrogen bonds : angle 4.48160 / 3.02 ( 2397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8430 (ptm) cc_final: 0.8170 (ppp) REVERT: A 602 MET cc_start: 0.9015 (tpp) cc_final: 0.8739 (tpp) REVERT: A 606 MET cc_start: 0.9314 (mmm) cc_final: 0.9024 (mmt) REVERT: B 126 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8760 (mtp) REVERT: B 567 MET cc_start: 0.9140 (mtp) cc_final: 0.8879 (mtp) REVERT: C 216 MET cc_start: 0.9559 (mmm) cc_final: 0.9194 (tpp) REVERT: D 456 MET cc_start: 0.9495 (mmm) cc_final: 0.9155 (mmt) REVERT: E 170 MET cc_start: 0.8095 (mmp) cc_final: 0.7875 (mpp) REVERT: E 309 MET cc_start: 0.6596 (mmt) cc_final: 0.5879 (tmm) REVERT: E 351 MET cc_start: 0.6018 (ptp) cc_final: 0.5287 (pmm) REVERT: E 435 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7420 (tm-30) outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.2995 time to fit residues: 50.3938 Evaluate side-chains 109 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 211 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 205 optimal weight: 0.0170 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 474 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.061553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.044826 restraints weight = 414565.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.046208 restraints weight = 192052.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045883 restraints weight = 113955.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.046132 restraints weight = 107358.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046037 restraints weight = 94678.051| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18116 Z= 0.168 Angle : 0.514 10.396 24370 Z= 0.279 Chirality : 0.047 1.412 2652 Planarity : 0.003 0.033 3127 Dihedral : 6.350 108.082 2416 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.66 % Allowed : 5.37 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2162 helix: 1.67 (0.17), residues: 977 sheet: -0.68 (0.30), residues: 273 loop : -0.73 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 612 TYR 0.011 0.001 TYR A 192 PHE 0.021 0.001 PHE E 287 TRP 0.011 0.001 TRP A 157 HIS 0.006 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (18116) covalent geometry : angle 0.51383 / 0.28 (24370) hydrogen bonds : bond 0.03477 / 2.33 ( 861) hydrogen bonds : angle 4.50615 / 3.04 ( 2397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8436 (ptm) cc_final: 0.8188 (ppp) REVERT: A 602 MET cc_start: 0.9057 (tpp) cc_final: 0.8773 (tpp) REVERT: A 606 MET cc_start: 0.9353 (mmm) cc_final: 0.9057 (mmt) REVERT: B 126 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8845 (mtp) REVERT: B 567 MET cc_start: 0.9159 (mtp) cc_final: 0.8906 (mtp) REVERT: C 216 MET cc_start: 0.9611 (mmm) cc_final: 0.9215 (tpp) REVERT: D 456 MET cc_start: 0.9514 (mmm) cc_final: 0.9172 (mmt) REVERT: E 351 MET cc_start: 0.6365 (ptp) cc_final: 0.5547 (pmm) REVERT: E 435 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7363 (tm-30) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.2861 time to fit residues: 49.6285 Evaluate side-chains 110 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 147 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.061022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044089 restraints weight = 422071.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045559 restraints weight = 195941.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.045996 restraints weight = 106044.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.046098 restraints weight = 94231.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046130 restraints weight = 84197.277| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18116 Z= 0.166 Angle : 0.509 10.396 24370 Z= 0.276 Chirality : 0.047 1.414 2652 Planarity : 0.003 0.028 3127 Dihedral : 6.253 107.940 2416 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.87 % Allowed : 5.42 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2162 helix: 1.73 (0.17), residues: 977 sheet: -0.59 (0.31), residues: 262 loop : -0.75 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 612 TYR 0.011 0.001 TYR A 192 PHE 0.021 0.001 PHE E 287 TRP 0.011 0.001 TRP A 157 HIS 0.006 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (18116) covalent geometry : angle 0.50949 / 0.28 (24370) hydrogen bonds : bond 0.03393 / 2.28 ( 861) hydrogen bonds : angle 4.48519 / 3.03 ( 2397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8551 (ptm) cc_final: 0.8168 (ptm) REVERT: A 602 MET cc_start: 0.9124 (tpp) cc_final: 0.8633 (tpp) REVERT: B 126 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8856 (mtp) REVERT: B 567 MET cc_start: 0.9205 (mtp) cc_final: 0.8927 (mtp) REVERT: C 57 CYS cc_start: 0.3826 (OUTLIER) cc_final: 0.2939 (t) REVERT: C 216 MET cc_start: 0.9616 (mmm) cc_final: 0.9223 (tpp) REVERT: D 456 MET cc_start: 0.9532 (mmm) cc_final: 0.9183 (mmt) REVERT: E 316 GLU cc_start: 0.8527 (tp30) cc_final: 0.8315 (tp30) REVERT: E 327 MET cc_start: 0.9211 (tpt) cc_final: 0.8951 (mmt) REVERT: E 435 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7368 (tm-30) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.2932 time to fit residues: 51.1092 Evaluate side-chains 116 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 435 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 170 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.061982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.044598 restraints weight = 408536.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046494 restraints weight = 191008.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.046384 restraints weight = 102292.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046460 restraints weight = 91334.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046583 restraints weight = 89469.484| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18116 Z= 0.097 Angle : 0.488 10.422 24370 Z= 0.261 Chirality : 0.047 1.428 2652 Planarity : 0.003 0.026 3127 Dihedral : 6.055 105.389 2416 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.61 % Allowed : 5.62 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2162 helix: 1.88 (0.17), residues: 980 sheet: -0.54 (0.31), residues: 262 loop : -0.61 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 612 TYR 0.009 0.001 TYR B 373 PHE 0.016 0.001 PHE E 190 TRP 0.011 0.001 TRP A 157 HIS 0.004 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (18116) covalent geometry : angle 0.48834 / 0.26 (24370) hydrogen bonds : bond 0.03212 / 2.15 ( 861) hydrogen bonds : angle 4.31970 / 2.90 ( 2397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.8510 (ptm) cc_final: 0.8240 (ppp) REVERT: A 602 MET cc_start: 0.9029 (tpp) cc_final: 0.8629 (tpp) REVERT: B 126 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8786 (mtp) REVERT: B 567 MET cc_start: 0.9165 (mtp) cc_final: 0.8895 (mtp) REVERT: C 57 CYS cc_start: 0.3588 (OUTLIER) cc_final: 0.2721 (t) REVERT: C 216 MET cc_start: 0.9575 (mmm) cc_final: 0.9275 (ttm) REVERT: D 456 MET cc_start: 0.9539 (mmm) cc_final: 0.9187 (mmt) REVERT: E 195 MET cc_start: 0.9544 (ptp) cc_final: 0.9318 (ppp) REVERT: E 287 PHE cc_start: 0.8918 (m-80) cc_final: 0.8687 (m-80) REVERT: E 327 MET cc_start: 0.9207 (tpt) cc_final: 0.8932 (mmt) REVERT: E 351 MET cc_start: 0.6111 (ptp) cc_final: 0.5384 (pmm) REVERT: E 435 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7401 (tm-30) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.2985 time to fit residues: 50.5356 Evaluate side-chains 110 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 117 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.060143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043334 restraints weight = 425269.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045186 restraints weight = 199363.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045137 restraints weight = 107579.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045267 restraints weight = 93642.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045441 restraints weight = 87790.812| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18116 Z= 0.222 Angle : 0.549 10.327 24370 Z= 0.298 Chirality : 0.047 1.397 2652 Planarity : 0.003 0.029 3127 Dihedral : 6.285 110.860 2416 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.66 % Allowed : 5.52 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2162 helix: 1.67 (0.17), residues: 977 sheet: -0.71 (0.31), residues: 263 loop : -0.77 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 30 TYR 0.014 0.001 TYR A 134 PHE 0.017 0.001 PHE E 190 TRP 0.009 0.001 TRP A 157 HIS 0.008 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (18116) covalent geometry : angle 0.54894 / 0.30 (24370) hydrogen bonds : bond 0.03465 / 2.33 ( 861) hydrogen bonds : angle 4.55420 / 3.08 ( 2397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.9093 (tpp) cc_final: 0.8721 (tpp) REVERT: B 126 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8824 (mtp) REVERT: B 567 MET cc_start: 0.9154 (mtp) cc_final: 0.8913 (mtp) REVERT: C 216 MET cc_start: 0.9594 (mmm) cc_final: 0.9181 (tpp) REVERT: D 456 MET cc_start: 0.9506 (mmm) cc_final: 0.9152 (mmt) REVERT: D 519 MET cc_start: 0.9230 (tpp) cc_final: 0.8947 (tpp) REVERT: E 287 PHE cc_start: 0.8904 (m-80) cc_final: 0.8666 (m-80) REVERT: E 316 GLU cc_start: 0.8434 (tp30) cc_final: 0.8215 (tp30) REVERT: E 327 MET cc_start: 0.9218 (tpt) cc_final: 0.8929 (tpt) REVERT: E 344 ILE cc_start: 0.8919 (mt) cc_final: 0.8707 (mm) REVERT: E 351 MET cc_start: 0.6625 (ptp) cc_final: 0.5982 (pmm) REVERT: E 435 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7314 (tm-30) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.3047 time to fit residues: 51.8421 Evaluate side-chains 111 residues out of total 1957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 276 TYR Chi-restraints excluded: chain B residue 607 LYS Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain D residue 432 HIS Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 382 CYS Chi-restraints excluded: chain E residue 435 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 96 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 214 optimal weight: 0.0170 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.060664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.043861 restraints weight = 423644.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045221 restraints weight = 176685.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.046060 restraints weight = 106718.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046487 restraints weight = 80650.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.046803 restraints weight = 69483.879| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18116 Z= 0.096 Angle : 0.497 10.424 24370 Z= 0.264 Chirality : 0.047 1.424 2652 Planarity : 0.003 0.026 3127 Dihedral : 6.006 105.614 2416 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.56 % Allowed : 5.77 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2162 helix: 1.87 (0.17), residues: 982 sheet: -0.58 (0.31), residues: 258 loop : -0.55 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 612 TYR 0.016 0.001 TYR E 313 PHE 0.016 0.001 PHE E 190 TRP 0.011 0.001 TRP B 158 HIS 0.004 0.001 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (18116) covalent geometry : angle 0.49680 / 0.26 (24370) hydrogen bonds : bond 0.03146 / 2.11 ( 861) hydrogen bonds : angle 4.29817 / 2.88 ( 2397) =============================================================================== Job complete usr+sys time: 5087.29 seconds wall clock time: 87 minutes 46.27 seconds (5266.27 seconds total)