Starting phenix.real_space_refine on Tue Jul 29 00:51:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.map" model { file = "/net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hrb_0258/07_2025/6hrb_0258.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6947 2.51 5 N 1818 2.21 5 O 1959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10787 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5008 Classifications: {'peptide': 674} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 646} Chain: "C" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1423 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.49, per 1000 atoms: 0.79 Number of scatterers: 10787 At special positions: 0 Unit cell: (88.044, 114.356, 161.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 61 16.00 P 1 15.00 O 1959 8.00 N 1818 7.00 C 6947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 60.7% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.548A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 4.116A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.626A pdb=" N ARG A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 81 removed outlier: 3.597A pdb=" N CYS A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 4.687A pdb=" N HIS A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.853A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.866A pdb=" N PHE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.603A pdb=" N ALA A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.845A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.545A pdb=" N THR A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 284 through 305 removed outlier: 3.613A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.421A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.556A pdb=" N VAL A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 Proline residue: A 362 - end of helix removed outlier: 3.546A pdb=" N GLN A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 399 removed outlier: 3.893A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 removed outlier: 4.027A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 4.009A pdb=" N VAL A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 3.756A pdb=" N THR A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.780A pdb=" N MET A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.805A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 removed outlier: 3.856A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 524 through 549 removed outlier: 3.729A pdb=" N GLY A 529 " --> pdb=" O PRO A 525 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Proline residue: A 545 - end of helix removed outlier: 3.749A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 11 through 24 removed outlier: 3.558A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.843A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 87 removed outlier: 3.626A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.618A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 removed outlier: 4.033A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 removed outlier: 3.578A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.672A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.619A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.707A pdb=" N GLU B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.732A pdb=" N LEU B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.023A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 408 removed outlier: 3.904A pdb=" N ILE B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 removed outlier: 4.008A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.600A pdb=" N GLN B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 removed outlier: 4.472A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 507 removed outlier: 3.525A pdb=" N LYS B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.502A pdb=" N ALA B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 557 through 591 removed outlier: 3.740A pdb=" N VAL B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 567 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.677A pdb=" N PHE B 595 " --> pdb=" O PRO B 592 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 596 " --> pdb=" O ALA B 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 596' Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.917A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.706A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 657 removed outlier: 3.939A pdb=" N LEU B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 removed outlier: 3.546A pdb=" N LEU B 662 " --> pdb=" O GLY B 658 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Proline residue: B 665 - end of helix removed outlier: 3.868A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 674 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.789A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 removed outlier: 4.339A pdb=" N LEU C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.523A pdb=" N ALA C 38 " --> pdb=" O PHE C 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 40 " --> pdb=" O TRP C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 34 through 40' Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.896A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.768A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.763A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 6 through 25 removed outlier: 4.126A pdb=" N TYR D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205 removed outlier: 3.527A pdb=" N GLN A 212 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 109 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.735A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.910A pdb=" N ASP B 550 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 removed outlier: 6.820A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.810A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 42 through 45 removed outlier: 5.706A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 132 523 hydrogen bonds defined for protein. 1515 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: 3.93 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3441 1.34 - 1.46: 1833 1.46 - 1.57: 5598 1.57 - 1.69: 4 1.69 - 1.81: 110 Bond restraints: 10986 Sorted by residual: bond pdb=" N ARG B 89 " pdb=" CA ARG B 89 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.25e+00 bond pdb=" CB VAL A 428 " pdb=" CG2 VAL A 428 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" C LEU A 213 " pdb=" N LEU A 214 " ideal model delta sigma weight residual 1.331 1.368 -0.037 2.07e-02 2.33e+03 3.19e+00 bond pdb=" CA ARG B 89 " pdb=" CB ARG B 89 " ideal model delta sigma weight residual 1.530 1.565 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C GLN C 164 " pdb=" N GLN C 165 " ideal model delta sigma weight residual 1.331 1.283 0.048 2.83e-02 1.25e+03 2.92e+00 ... (remaining 10981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 14668 2.82 - 5.63: 241 5.63 - 8.45: 36 8.45 - 11.26: 6 11.26 - 14.08: 3 Bond angle restraints: 14954 Sorted by residual: angle pdb=" C GLY B 88 " pdb=" N ARG B 89 " pdb=" CA ARG B 89 " ideal model delta sigma weight residual 121.70 135.78 -14.08 1.80e+00 3.09e-01 6.12e+01 angle pdb=" C MET A 360 " pdb=" N VAL A 361 " pdb=" CA VAL A 361 " ideal model delta sigma weight residual 120.24 124.03 -3.79 6.30e-01 2.52e+00 3.61e+01 angle pdb=" N ASN B 26 " pdb=" CA ASN B 26 " pdb=" C ASN B 26 " ideal model delta sigma weight residual 109.81 119.59 -9.78 2.21e+00 2.05e-01 1.96e+01 angle pdb=" C ALA B 319 " pdb=" N SER B 320 " pdb=" CA SER B 320 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" CB LEU A 133 " pdb=" CG LEU A 133 " pdb=" CD2 LEU A 133 " ideal model delta sigma weight residual 110.70 98.39 12.31 3.00e+00 1.11e-01 1.68e+01 ... (remaining 14949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 6245 15.50 - 31.01: 244 31.01 - 46.51: 36 46.51 - 62.01: 5 62.01 - 77.51: 3 Dihedral angle restraints: 6533 sinusoidal: 2436 harmonic: 4097 Sorted by residual: dihedral pdb=" CA ASN A 239 " pdb=" C ASN A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta harmonic sigma weight residual 180.00 148.70 31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA ALA B 319 " pdb=" C ALA B 319 " pdb=" N SER B 320 " pdb=" CA SER B 320 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 6530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1144 0.046 - 0.092: 499 0.092 - 0.138: 138 0.138 - 0.185: 16 0.185 - 0.231: 6 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA ARG B 89 " pdb=" N ARG B 89 " pdb=" C ARG B 89 " pdb=" CB ARG B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL B 449 " pdb=" CA VAL B 449 " pdb=" CG1 VAL B 449 " pdb=" CG2 VAL B 449 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1800 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 424 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 425 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 240 " -0.041 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO B 241 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO B 524 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " -0.034 5.00e-02 4.00e+02 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 2659 2.78 - 3.37: 12152 3.37 - 3.96: 20687 3.96 - 4.55: 29120 4.55 - 5.14: 41922 Nonbonded interactions: 106540 Sorted by model distance: nonbonded pdb=" O ASP B 307 " pdb=" OG1 THR B 311 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.246 3.040 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.262 3.040 nonbonded pdb=" O MET A 130 " pdb=" OG1 THR A 134 " model vdw 2.264 3.040 ... (remaining 106535 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 135.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.930 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.008 0.085 10986 Z= 0.337 Angle : 0.963 14.078 14954 Z= 0.499 Chirality : 0.054 0.231 1803 Planarity : 0.007 0.087 1898 Dihedral : 9.280 77.514 3901 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.26 % Allowed : 1.50 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.16), residues: 1436 helix: -3.80 (0.10), residues: 765 sheet: -2.20 (0.46), residues: 91 loop : -2.48 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 245 HIS 0.012 0.002 HIS A 451 PHE 0.025 0.003 PHE A 471 TYR 0.015 0.003 TYR A 201 ARG 0.019 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.29646 ( 523) hydrogen bonds : angle 10.20594 ( 1515) covalent geometry : bond 0.00776 (10986) covalent geometry : angle 0.96308 (14954) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8870 (p0) cc_final: 0.8537 (p0) REVERT: A 167 TRP cc_start: 0.8897 (m100) cc_final: 0.8258 (m100) REVERT: A 175 LEU cc_start: 0.9369 (mt) cc_final: 0.8536 (tp) REVERT: A 227 MET cc_start: 0.8998 (mmm) cc_final: 0.8195 (mmt) REVERT: A 287 MET cc_start: 0.9044 (mtm) cc_final: 0.8481 (mtp) REVERT: A 320 MET cc_start: 0.8796 (mmm) cc_final: 0.8336 (tpp) REVERT: A 366 MET cc_start: 0.9280 (mtm) cc_final: 0.8999 (mtm) REVERT: A 392 PHE cc_start: 0.8360 (t80) cc_final: 0.7865 (t80) REVERT: A 469 SER cc_start: 0.9426 (m) cc_final: 0.8875 (p) REVERT: A 510 LYS cc_start: 0.8642 (mttm) cc_final: 0.8434 (mtpt) REVERT: A 537 LEU cc_start: 0.8895 (tp) cc_final: 0.8646 (tp) REVERT: A 541 LEU cc_start: 0.9595 (mt) cc_final: 0.9295 (mp) REVERT: B 371 HIS cc_start: 0.8348 (m-70) cc_final: 0.8106 (m-70) REVERT: C 22 TYR cc_start: 0.9150 (t80) cc_final: 0.8749 (t80) REVERT: C 48 THR cc_start: 0.9290 (p) cc_final: 0.8427 (p) REVERT: D 14 LEU cc_start: 0.9444 (mt) cc_final: 0.9117 (tt) REVERT: D 21 TYR cc_start: 0.9335 (t80) cc_final: 0.8894 (t80) outliers start: 3 outliers final: 1 residues processed: 242 average time/residue: 0.3135 time to fit residues: 107.3711 Evaluate side-chains 126 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 HIS A 466 ASN B 316 ASN B 326 GLN B 404 HIS B 536 ASN B 547 ASN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN C 31 GLN C 154 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.047537 restraints weight = 49721.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.048938 restraints weight = 24344.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049785 restraints weight = 14658.053| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10986 Z= 0.163 Angle : 0.710 9.560 14954 Z= 0.362 Chirality : 0.043 0.196 1803 Planarity : 0.005 0.048 1898 Dihedral : 5.637 23.919 1525 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 9.18 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.19), residues: 1436 helix: -1.82 (0.15), residues: 822 sheet: -1.94 (0.44), residues: 104 loop : -2.08 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 176 HIS 0.002 0.001 HIS A 523 PHE 0.018 0.002 PHE A 138 TYR 0.020 0.002 TYR A 381 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 523) hydrogen bonds : angle 5.49868 ( 1515) covalent geometry : bond 0.00359 (10986) covalent geometry : angle 0.71007 (14954) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8837 (p0) cc_final: 0.8244 (p0) REVERT: A 167 TRP cc_start: 0.8917 (m100) cc_final: 0.8308 (m100) REVERT: A 176 TRP cc_start: 0.8121 (m100) cc_final: 0.7237 (m100) REVERT: A 367 GLN cc_start: 0.8542 (mt0) cc_final: 0.8339 (mp10) REVERT: A 392 PHE cc_start: 0.8380 (t80) cc_final: 0.7832 (t80) REVERT: A 489 MET cc_start: 0.9192 (mtm) cc_final: 0.8818 (mtm) REVERT: A 537 LEU cc_start: 0.8949 (tp) cc_final: 0.8674 (tp) REVERT: A 541 LEU cc_start: 0.9611 (mt) cc_final: 0.9355 (mp) REVERT: B 371 HIS cc_start: 0.8160 (m-70) cc_final: 0.7943 (m-70) REVERT: B 383 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7424 (mtm) REVERT: C 10 THR cc_start: 0.9348 (m) cc_final: 0.9003 (m) REVERT: C 74 GLU cc_start: 0.8080 (tp30) cc_final: 0.7730 (tp30) REVERT: C 129 ASP cc_start: 0.8475 (t0) cc_final: 0.8247 (t0) outliers start: 24 outliers final: 8 residues processed: 175 average time/residue: 0.3240 time to fit residues: 87.5812 Evaluate side-chains 128 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 19 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN B 16 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.047568 restraints weight = 50512.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.048976 restraints weight = 24712.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049912 restraints weight = 14775.887| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10986 Z= 0.142 Angle : 0.652 9.462 14954 Z= 0.324 Chirality : 0.041 0.229 1803 Planarity : 0.004 0.048 1898 Dihedral : 5.145 22.579 1524 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.50 % Allowed : 11.65 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1436 helix: -0.88 (0.17), residues: 825 sheet: -1.74 (0.44), residues: 107 loop : -1.87 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 176 HIS 0.003 0.001 HIS B 563 PHE 0.021 0.002 PHE A 138 TYR 0.016 0.002 TYR A 381 ARG 0.002 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 523) hydrogen bonds : angle 4.96812 ( 1515) covalent geometry : bond 0.00330 (10986) covalent geometry : angle 0.65235 (14954) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8889 (p0) cc_final: 0.8187 (p0) REVERT: A 167 TRP cc_start: 0.8971 (m100) cc_final: 0.8144 (m100) REVERT: A 176 TRP cc_start: 0.8158 (m100) cc_final: 0.7952 (m100) REVERT: A 245 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8385 (mt-10) REVERT: A 537 LEU cc_start: 0.9023 (tp) cc_final: 0.8641 (tp) REVERT: A 541 LEU cc_start: 0.9613 (mt) cc_final: 0.9373 (mp) REVERT: B 371 HIS cc_start: 0.8145 (m-70) cc_final: 0.7902 (m-70) REVERT: B 383 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7274 (mtm) REVERT: B 649 MET cc_start: 0.8716 (tpp) cc_final: 0.8436 (ttp) REVERT: C 10 THR cc_start: 0.9314 (m) cc_final: 0.8894 (m) REVERT: C 75 MET cc_start: 0.8177 (pmm) cc_final: 0.7916 (pmm) REVERT: C 119 GLU cc_start: 0.8864 (mp0) cc_final: 0.8567 (mt-10) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.1944 time to fit residues: 47.0095 Evaluate side-chains 129 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 383 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.045663 restraints weight = 50774.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047063 restraints weight = 25076.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047888 restraints weight = 14994.740| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10986 Z= 0.210 Angle : 0.687 8.949 14954 Z= 0.340 Chirality : 0.043 0.166 1803 Planarity : 0.003 0.048 1898 Dihedral : 5.024 22.387 1524 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.77 % Allowed : 12.27 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1436 helix: -0.31 (0.17), residues: 828 sheet: -1.52 (0.45), residues: 107 loop : -1.72 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 71 HIS 0.005 0.001 HIS A 451 PHE 0.021 0.002 PHE A 127 TYR 0.021 0.002 TYR A 458 ARG 0.003 0.000 ARG B 425 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 523) hydrogen bonds : angle 4.80355 ( 1515) covalent geometry : bond 0.00472 (10986) covalent geometry : angle 0.68673 (14954) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9040 (p0) cc_final: 0.8408 (p0) REVERT: A 256 MET cc_start: 0.8964 (mmm) cc_final: 0.8710 (mtt) REVERT: A 458 TYR cc_start: 0.9438 (t80) cc_final: 0.9130 (t80) REVERT: A 489 MET cc_start: 0.9171 (mtm) cc_final: 0.8885 (mtm) REVERT: A 537 LEU cc_start: 0.9046 (tp) cc_final: 0.8675 (tp) REVERT: A 541 LEU cc_start: 0.9603 (mt) cc_final: 0.9318 (mp) REVERT: B 371 HIS cc_start: 0.8234 (m-70) cc_final: 0.7974 (m-70) REVERT: B 383 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7301 (mtm) REVERT: B 649 MET cc_start: 0.8821 (tpp) cc_final: 0.8619 (tpp) REVERT: C 74 GLU cc_start: 0.8367 (tp30) cc_final: 0.8148 (tp30) REVERT: C 75 MET cc_start: 0.8422 (pmm) cc_final: 0.8109 (pmm) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 0.1739 time to fit residues: 36.4569 Evaluate side-chains 123 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 3 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 338 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.048034 restraints weight = 50168.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049498 restraints weight = 24275.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050443 restraints weight = 14291.845| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10986 Z= 0.111 Angle : 0.604 9.083 14954 Z= 0.297 Chirality : 0.041 0.195 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.740 22.856 1524 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 13.06 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1436 helix: 0.16 (0.18), residues: 832 sheet: -1.31 (0.46), residues: 106 loop : -1.73 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 PHE 0.015 0.001 PHE A 127 TYR 0.019 0.002 TYR B 641 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 523) hydrogen bonds : angle 4.51431 ( 1515) covalent geometry : bond 0.00256 (10986) covalent geometry : angle 0.60435 (14954) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8989 (p0) cc_final: 0.8222 (p0) REVERT: A 227 MET cc_start: 0.8285 (mmm) cc_final: 0.8052 (mmm) REVERT: A 380 LEU cc_start: 0.9423 (tp) cc_final: 0.9159 (tp) REVERT: A 469 SER cc_start: 0.9245 (m) cc_final: 0.9016 (p) REVERT: A 537 LEU cc_start: 0.8956 (tp) cc_final: 0.8589 (tp) REVERT: A 541 LEU cc_start: 0.9605 (mt) cc_final: 0.9338 (mp) REVERT: B 221 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9158 (tt) REVERT: B 371 HIS cc_start: 0.8189 (m-70) cc_final: 0.7966 (m-70) REVERT: B 383 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: B 649 MET cc_start: 0.8748 (tpp) cc_final: 0.8520 (tpp) REVERT: C 22 TYR cc_start: 0.8951 (t80) cc_final: 0.8700 (t80) REVERT: C 74 GLU cc_start: 0.8319 (tp30) cc_final: 0.8046 (tp30) REVERT: C 75 MET cc_start: 0.8384 (pmm) cc_final: 0.8069 (pmm) outliers start: 22 outliers final: 7 residues processed: 154 average time/residue: 0.2434 time to fit residues: 57.6401 Evaluate side-chains 127 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 383 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.047617 restraints weight = 50968.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.049058 restraints weight = 24962.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049967 restraints weight = 14866.970| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.003 0.040 10986 Z= 0.128 Angle : 0.621 9.186 14954 Z= 0.304 Chirality : 0.041 0.200 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.627 24.271 1524 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.85 % Allowed : 14.12 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1436 helix: 0.39 (0.18), residues: 839 sheet: -1.15 (0.47), residues: 106 loop : -1.73 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.045 0.001 PHE A 109 TYR 0.014 0.001 TYR A 381 ARG 0.001 0.000 ARG B 212 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 523) hydrogen bonds : angle 4.44156 ( 1515) covalent geometry : bond 0.00299 (10986) covalent geometry : angle 0.62110 (14954) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9017 (p0) cc_final: 0.8253 (p0) REVERT: A 227 MET cc_start: 0.8341 (mmm) cc_final: 0.8138 (mmm) REVERT: A 469 SER cc_start: 0.9323 (m) cc_final: 0.9034 (p) REVERT: A 489 MET cc_start: 0.9017 (mtm) cc_final: 0.8719 (mtm) REVERT: A 537 LEU cc_start: 0.8999 (tp) cc_final: 0.8634 (tp) REVERT: A 541 LEU cc_start: 0.9600 (mt) cc_final: 0.9316 (mp) REVERT: B 221 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9138 (tt) REVERT: B 371 HIS cc_start: 0.8307 (m-70) cc_final: 0.8039 (m-70) REVERT: B 383 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7270 (mtm) REVERT: B 649 MET cc_start: 0.8772 (tpp) cc_final: 0.8529 (tpp) REVERT: C 18 THR cc_start: 0.8766 (p) cc_final: 0.8471 (m) REVERT: C 74 GLU cc_start: 0.8378 (tp30) cc_final: 0.8107 (tp30) REVERT: C 75 MET cc_start: 0.8437 (pmm) cc_final: 0.8151 (pmm) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 0.2416 time to fit residues: 52.4505 Evaluate side-chains 132 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.047721 restraints weight = 51222.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049160 restraints weight = 25053.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.050103 restraints weight = 14902.368| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10986 Z= 0.128 Angle : 0.620 9.862 14954 Z= 0.304 Chirality : 0.041 0.168 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.571 25.526 1524 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.94 % Allowed : 14.65 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1436 helix: 0.52 (0.18), residues: 841 sheet: -1.04 (0.48), residues: 106 loop : -1.66 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.041 0.001 PHE A 109 TYR 0.026 0.002 TYR B 641 ARG 0.004 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 523) hydrogen bonds : angle 4.37478 ( 1515) covalent geometry : bond 0.00299 (10986) covalent geometry : angle 0.62021 (14954) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9020 (p0) cc_final: 0.8215 (p0) REVERT: A 225 ILE cc_start: 0.8373 (mt) cc_final: 0.7954 (mt) REVERT: A 380 LEU cc_start: 0.9360 (tp) cc_final: 0.9045 (tp) REVERT: A 426 THR cc_start: 0.8639 (m) cc_final: 0.8311 (m) REVERT: A 439 ASP cc_start: 0.8463 (p0) cc_final: 0.8096 (t70) REVERT: A 469 SER cc_start: 0.9346 (m) cc_final: 0.9039 (p) REVERT: A 537 LEU cc_start: 0.8956 (tp) cc_final: 0.8503 (tp) REVERT: B 203 MET cc_start: 0.9248 (tpt) cc_final: 0.9014 (tpp) REVERT: B 221 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9150 (tt) REVERT: B 371 HIS cc_start: 0.8216 (m-70) cc_final: 0.7962 (m-70) REVERT: B 383 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7237 (mtm) REVERT: B 649 MET cc_start: 0.8795 (tpp) cc_final: 0.8535 (tpp) REVERT: C 74 GLU cc_start: 0.8383 (tp30) cc_final: 0.8158 (tp30) REVERT: C 75 MET cc_start: 0.8471 (pmm) cc_final: 0.8204 (pmm) REVERT: C 119 GLU cc_start: 0.8939 (mp0) cc_final: 0.8369 (mt-10) REVERT: C 180 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8030 (mm-30) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.1818 time to fit residues: 39.9346 Evaluate side-chains 133 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048904 restraints weight = 50131.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.050336 restraints weight = 24455.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051301 restraints weight = 14569.563| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10986 Z= 0.113 Angle : 0.623 9.185 14954 Z= 0.303 Chirality : 0.041 0.159 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.509 26.908 1524 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.68 % Allowed : 15.18 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1436 helix: 0.69 (0.18), residues: 844 sheet: -0.93 (0.48), residues: 106 loop : -1.54 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 176 HIS 0.002 0.000 HIS A 451 PHE 0.030 0.001 PHE A 109 TYR 0.025 0.002 TYR B 641 ARG 0.003 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 523) hydrogen bonds : angle 4.24104 ( 1515) covalent geometry : bond 0.00262 (10986) covalent geometry : angle 0.62316 (14954) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9018 (p0) cc_final: 0.8229 (p0) REVERT: A 380 LEU cc_start: 0.9377 (tp) cc_final: 0.9024 (tp) REVERT: A 426 THR cc_start: 0.8558 (m) cc_final: 0.8201 (m) REVERT: A 439 ASP cc_start: 0.8433 (p0) cc_final: 0.8085 (t70) REVERT: A 537 LEU cc_start: 0.8899 (tp) cc_final: 0.8424 (tp) REVERT: B 383 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7211 (mtm) REVERT: B 649 MET cc_start: 0.8750 (tpp) cc_final: 0.8471 (tpp) REVERT: C 74 GLU cc_start: 0.8381 (tp30) cc_final: 0.8134 (tp30) REVERT: C 75 MET cc_start: 0.8491 (pmm) cc_final: 0.8223 (pmm) REVERT: C 129 ASP cc_start: 0.8172 (t0) cc_final: 0.7970 (t0) REVERT: C 180 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7976 (mm-30) outliers start: 19 outliers final: 13 residues processed: 146 average time/residue: 0.2210 time to fit residues: 52.0062 Evaluate side-chains 136 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 634 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** 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 = 0.3113 r_free = 0.3113 target = 0.058315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047639 restraints weight = 51562.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.049043 restraints weight = 25587.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.049933 restraints weight = 15404.914| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10986 Z= 0.148 Angle : 0.667 10.976 14954 Z= 0.321 Chirality : 0.042 0.239 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.471 27.807 1524 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.68 % Allowed : 16.42 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1436 helix: 0.78 (0.18), residues: 843 sheet: -0.88 (0.49), residues: 106 loop : -1.58 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.024 0.001 PHE A 392 TYR 0.029 0.002 TYR B 641 ARG 0.006 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 523) hydrogen bonds : angle 4.28022 ( 1515) covalent geometry : bond 0.00347 (10986) covalent geometry : angle 0.66704 (14954) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.9035 (p0) cc_final: 0.8300 (p0) REVERT: A 256 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8281 (ttm) REVERT: A 380 LEU cc_start: 0.9420 (tp) cc_final: 0.9054 (tp) REVERT: A 426 THR cc_start: 0.8625 (m) cc_final: 0.8288 (m) REVERT: A 439 ASP cc_start: 0.8498 (p0) cc_final: 0.8087 (t70) REVERT: A 537 LEU cc_start: 0.8939 (tp) cc_final: 0.8419 (tp) REVERT: B 383 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7223 (mtm) REVERT: C 74 GLU cc_start: 0.8417 (tp30) cc_final: 0.8191 (tp30) REVERT: C 75 MET cc_start: 0.8511 (pmm) cc_final: 0.8244 (pmm) REVERT: C 119 GLU cc_start: 0.8874 (mp0) cc_final: 0.8373 (mt-10) REVERT: C 180 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8023 (mm-30) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.3433 time to fit residues: 72.0503 Evaluate side-chains 134 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain C residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 17 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** 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 = 0.3132 r_free = 0.3132 target = 0.059046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048368 restraints weight = 50746.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049782 restraints weight = 25103.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050711 restraints weight = 15064.581| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10986 Z= 0.130 Angle : 0.663 10.998 14954 Z= 0.319 Chirality : 0.042 0.235 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.499 28.898 1524 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.59 % Allowed : 16.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1436 helix: 0.81 (0.18), residues: 839 sheet: -0.83 (0.49), residues: 106 loop : -1.54 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 176 HIS 0.002 0.001 HIS A 451 PHE 0.040 0.002 PHE A 109 TYR 0.023 0.002 TYR B 641 ARG 0.003 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 523) hydrogen bonds : angle 4.24348 ( 1515) covalent geometry : bond 0.00307 (10986) covalent geometry : angle 0.66291 (14954) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8964 (p0) cc_final: 0.8202 (p0) REVERT: A 151 LEU cc_start: 0.9237 (tp) cc_final: 0.9032 (tt) REVERT: A 287 MET cc_start: 0.8825 (mtt) cc_final: 0.8390 (ttm) REVERT: A 380 LEU cc_start: 0.9339 (tp) cc_final: 0.8975 (tp) REVERT: A 426 THR cc_start: 0.8633 (m) cc_final: 0.8288 (m) REVERT: A 439 ASP cc_start: 0.8495 (p0) cc_final: 0.8078 (t70) REVERT: A 537 LEU cc_start: 0.8868 (tp) cc_final: 0.8463 (tp) REVERT: B 383 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7197 (mtm) REVERT: C 75 MET cc_start: 0.8543 (pmm) cc_final: 0.8272 (pmm) REVERT: C 119 GLU cc_start: 0.8908 (mp0) cc_final: 0.8403 (mt-10) REVERT: C 129 ASP cc_start: 0.8154 (t0) cc_final: 0.7849 (t0) REVERT: C 180 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8001 (mm-30) outliers start: 18 outliers final: 11 residues processed: 138 average time/residue: 0.3090 time to fit residues: 69.2294 Evaluate side-chains 130 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain D residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 139 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.048952 restraints weight = 50687.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.050385 restraints weight = 25042.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051325 restraints weight = 14970.598| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10986 Z= 0.119 Angle : 0.664 11.081 14954 Z= 0.317 Chirality : 0.042 0.222 1803 Planarity : 0.003 0.050 1898 Dihedral : 4.488 29.895 1524 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.68 % Allowed : 16.86 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1436 helix: 0.82 (0.18), residues: 839 sheet: -0.80 (0.49), residues: 106 loop : -1.55 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 176 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.001 PHE A 109 TYR 0.024 0.002 TYR B 641 ARG 0.002 0.000 ARG A 153 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 523) hydrogen bonds : angle 4.22499 ( 1515) covalent geometry : bond 0.00278 (10986) covalent geometry : angle 0.66388 (14954) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.30 seconds wall clock time: 84 minutes 23.73 seconds (5063.73 seconds total)