Starting phenix.real_space_refine on Sun Sep 13 19:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wqh_21870/09_2026/6wqh_21870.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 S 99 5.16 5 B 6 2.79 5 C 16078 2.51 5 N 4448 2.21 5 O 4827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25471 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 2, 'PTRANS': 34, 'TRANS': 500} Chain breaks: 1 Chain: "C" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4188 Classifications: {'peptide': 538} Link IDs: {'CIS': 2, 'PTRANS': 34, 'TRANS': 501} Chain breaks: 1 Chain: "F" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain: "D" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "E" Number of atoms: 4179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4179 Classifications: {'peptide': 537} Link IDs: {'CIS': 3, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 1 Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'4KZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.23 Number of scatterers: 25471 At special positions: 0 Unit cell: (131.3, 148.85, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 13 15.00 O 4827 8.00 N 4448 7.00 C 16078 6.00 B 6 5.00 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 Atom "HETATM25162 O3B AGS A 801 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 30 sheets defined 46.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.635A pdb=" N ARG A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 4.842A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.712A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.696A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 338 removed outlier: 3.644A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.819A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 4.331A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.759A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 4.293A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 447 through 450 Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.862A pdb=" N THR A 476 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.942A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.785A pdb=" N ALA A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 513 removed outlier: 3.592A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.840A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 561 removed outlier: 3.923A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 656 through 659 removed outlier: 3.617A pdb=" N ASN A 659 " --> pdb=" O ASP A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 680 through 693 Processing helix chain 'A' and resid 718 through 728 removed outlier: 3.527A pdb=" N LEU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.980A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 742 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 743 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 4.175A pdb=" N GLU A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 770 removed outlier: 3.788A pdb=" N TYR A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.862A pdb=" N LEU B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 282 through 294 removed outlier: 4.489A pdb=" N TYR B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 322 through 338 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.675A pdb=" N MET B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 437 Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.055A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.523A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.528A pdb=" N LYS B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 514 removed outlier: 3.619A pdb=" N GLU B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 4.118A pdb=" N VAL B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.657A pdb=" N LYS B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.623A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.809A pdb=" N LYS B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 660' Processing helix chain 'B' and resid 679 through 692 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.602A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.604A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.953A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 removed outlier: 3.513A pdb=" N VAL C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 4.488A pdb=" N GLU C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.912A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.532A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 338 removed outlier: 3.688A pdb=" N TYR C 332 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 373 removed outlier: 4.177A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 removed outlier: 3.651A pdb=" N MET C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 443 removed outlier: 3.776A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 removed outlier: 5.918A pdb=" N ASN C 449 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 512 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.862A pdb=" N LEU C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 561 removed outlier: 3.961A pdb=" N ARG C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 561 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.547A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.727A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 679 through 693 removed outlier: 3.645A pdb=" N THR C 685 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.586A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.471A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 4.026A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.948A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 256 removed outlier: 4.802A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 262 Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.712A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 273 removed outlier: 3.640A pdb=" N ARG F 272 " --> pdb=" O LYS F 268 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 273' Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.674A pdb=" N LEU F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP F 292 " --> pdb=" O THR F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 removed outlier: 4.164A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 334 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.619A pdb=" N LEU F 338 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.567A pdb=" N ALA F 408 " --> pdb=" O LYS F 404 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 4.395A pdb=" N MET F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 441 " --> pdb=" O SER F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 Processing helix chain 'F' and resid 496 through 505 removed outlier: 3.787A pdb=" N ALA F 502 " --> pdb=" O LYS F 498 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 Processing helix chain 'F' and resid 513 through 515 No H-bonds generated for 'chain 'F' and resid 513 through 515' Processing helix chain 'F' and resid 523 through 533 removed outlier: 3.624A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 529 " --> pdb=" O ALA F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 561 removed outlier: 3.551A pdb=" N GLU F 544 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP F 558 " --> pdb=" O GLY F 554 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 559 " --> pdb=" O ALA F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 579 Processing helix chain 'F' and resid 630 through 646 removed outlier: 3.558A pdb=" N GLN F 638 " --> pdb=" O LYS F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 660 Processing helix chain 'F' and resid 676 through 678 No H-bonds generated for 'chain 'F' and resid 676 through 678' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 728 Processing helix chain 'F' and resid 738 through 746 removed outlier: 3.578A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 746 " --> pdb=" O LEU F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 754 Processing helix chain 'F' and resid 761 through 770 removed outlier: 3.908A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 254 removed outlier: 3.514A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.579A pdb=" N GLU D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.560A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.132A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 4.231A pdb=" N GLU D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.835A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 443 removed outlier: 4.323A pdb=" N VAL D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 3.546A pdb=" N ASN D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 484 removed outlier: 3.644A pdb=" N LEU D 482 " --> pdb=" O PRO D 478 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 removed outlier: 4.350A pdb=" N ARG D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 515 removed outlier: 3.992A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.770A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.955A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 549 " --> pdb=" O ARG D 545 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.587A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 Processing helix chain 'D' and resid 654 through 659 removed outlier: 4.139A pdb=" N TYR D 658 " --> pdb=" O GLU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 718 through 728 Processing helix chain 'D' and resid 738 through 746 removed outlier: 4.399A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.623A pdb=" N GLU D 752 " --> pdb=" O LYS D 748 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 754 " --> pdb=" O VAL D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.672A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.679A pdb=" N ALA E 248 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 249 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 267 Processing helix chain 'E' and resid 272 through 276 removed outlier: 4.423A pdb=" N ARG E 275 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET E 276 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 276' Processing helix chain 'E' and resid 285 through 294 removed outlier: 4.357A pdb=" N ASP E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 removed outlier: 3.622A pdb=" N THR E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 315 " --> pdb=" O THR E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 removed outlier: 4.222A pdb=" N TYR E 332 " --> pdb=" O ARG E 328 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 370 removed outlier: 3.846A pdb=" N ARG E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E 369 " --> pdb=" O GLY E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 434 through 444 removed outlier: 3.575A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.809A pdb=" N PHE E 451 " --> pdb=" O ASN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 494 through 505 removed outlier: 3.540A pdb=" N GLN E 499 " --> pdb=" O ASN E 495 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 501 " --> pdb=" O GLU E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 515 removed outlier: 4.249A pdb=" N GLN E 510 " --> pdb=" O LEU E 506 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL E 511 " --> pdb=" O TRP E 507 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG E 512 " --> pdb=" O PRO E 508 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU E 513 " --> pdb=" O LYS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 533 removed outlier: 3.768A pdb=" N LEU E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG E 529 " --> pdb=" O ALA E 525 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL E 530 " --> pdb=" O ALA E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.649A pdb=" N ALA E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA E 555 " --> pdb=" O ALA E 551 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS E 556 " --> pdb=" O ARG E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 630 through 646 removed outlier: 3.738A pdb=" N SER E 636 " --> pdb=" O VAL E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 Processing helix chain 'E' and resid 738 through 746 removed outlier: 4.281A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 761 through 770 removed outlier: 4.003A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 468 through 471 removed outlier: 6.624A pdb=" N LEU A 351 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 471 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA3, first strand: chain 'A' and resid 451 through 452 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.642A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 625 removed outlier: 6.763A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 617 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ILE A 700 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 598 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 702 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 600 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.347A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 520 through 522 removed outlier: 7.408A pdb=" N GLU B 521 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611 removed outlier: 6.347A pdb=" N GLN B 598 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 618 Processing sheet with id=AB2, first strand: chain 'B' and resid 705 through 706 removed outlier: 3.618A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB4, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.847A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 622 through 626 removed outlier: 8.993A pdb=" N ILE C 700 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN C 598 " --> pdb=" O ILE C 700 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 702 " --> pdb=" O GLN C 598 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 705 through 706 removed outlier: 3.655A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 378 through 379 removed outlier: 3.572A pdb=" N ILE F 468 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR F 470 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AB9, first strand: chain 'F' and resid 623 through 626 removed outlier: 3.683A pdb=" N SER F 624 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N MET F 702 " --> pdb=" O THR F 596 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN F 598 " --> pdb=" O MET F 702 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE F 733 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL F 759 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU F 735 " --> pdb=" O VAL F 759 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 705 through 706 removed outlier: 3.680A pdb=" N GLU F 705 " --> pdb=" O MET F 713 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 376 through 380 removed outlier: 3.804A pdb=" N ILE D 468 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 352 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC4, first strand: chain 'D' and resid 593 through 594 removed outlier: 3.718A pdb=" N GLN D 593 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 617 through 618 removed outlier: 6.879A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 617 through 618 removed outlier: 10.227A pdb=" N THR D 596 " --> pdb=" O ILE D 700 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N MET D 702 " --> pdb=" O THR D 596 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN D 598 " --> pdb=" O MET D 702 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 705 through 706 Processing sheet with id=AC8, first strand: chain 'E' and resid 419 through 420 removed outlier: 6.689A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 520 through 522 Processing sheet with id=AD1, first strand: chain 'E' and resid 596 through 603 removed outlier: 6.541A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 700 through 702 Processing sheet with id=AD3, first strand: chain 'E' and resid 705 through 706 removed outlier: 3.949A pdb=" N GLU E 705 " --> pdb=" O MET E 713 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2499 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: 4.85 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.43: 10285 1.43 - 1.82: 15672 1.82 - 2.20: 3 2.20 - 2.59: 0 2.59 - 2.98: 1 Bond restraints: 25961 Sorted by residual: bond pdb=" C GLU F 589 " pdb=" N THR F 590 " ideal model delta sigma weight residual 1.332 2.975 -1.643 1.40e-02 5.10e+03 1.38e+04 bond pdb=" C GLY F 676 " pdb=" N PRO F 677 " ideal model delta sigma weight residual 1.332 1.769 -0.437 8.90e-03 1.26e+04 2.41e+03 bond pdb=" C GLY D 676 " pdb=" N PRO D 677 " ideal model delta sigma weight residual 1.333 1.711 -0.378 7.80e-03 1.64e+04 2.34e+03 bond pdb=" C GLY A 676 " pdb=" N PRO A 677 " ideal model delta sigma weight residual 1.331 1.649 -0.318 7.90e-03 1.60e+04 1.62e+03 bond pdb=" C GLY B 676 " pdb=" N PRO B 677 " ideal model delta sigma weight residual 1.333 1.159 0.174 7.80e-03 1.64e+04 4.99e+02 ... (remaining 25956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.79: 35210 14.79 - 29.57: 8 29.57 - 44.36: 0 44.36 - 59.15: 0 59.15 - 73.93: 1 Bond angle restraints: 35219 Sorted by residual: angle pdb=" O GLU F 589 " pdb=" C GLU F 589 " pdb=" N THR F 590 " ideal model delta sigma weight residual 122.11 48.18 73.93 1.18e+00 7.18e-01 3.93e+03 angle pdb=" O GLY A 676 " pdb=" C GLY A 676 " pdb=" N PRO A 677 " ideal model delta sigma weight residual 121.77 105.57 16.20 1.00e+00 1.00e+00 2.62e+02 angle pdb=" C GLY A 676 " pdb=" N PRO A 677 " pdb=" CA PRO A 677 " ideal model delta sigma weight residual 121.00 137.20 -16.20 1.16e+00 7.43e-01 1.95e+02 angle pdb=" C GLY D 676 " pdb=" N PRO D 677 " pdb=" CA PRO D 677 " ideal model delta sigma weight residual 120.94 136.21 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" O GLY D 676 " pdb=" C GLY D 676 " pdb=" N PRO D 677 " ideal model delta sigma weight residual 121.77 110.81 10.96 1.00e+00 1.00e+00 1.20e+02 ... (remaining 35214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.20: 15366 31.20 - 62.40: 518 62.40 - 93.59: 71 93.59 - 124.79: 1 124.79 - 155.99: 2 Dihedral angle restraints: 15958 sinusoidal: 6706 harmonic: 9252 Sorted by residual: dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 163.55 136.46 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C5' ADP F 801 " pdb=" O5' ADP F 801 " pdb=" PA ADP F 801 " pdb=" O2A ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 -179.77 119.77 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA GLN C 278 " pdb=" C GLN C 278 " pdb=" N GLY C 279 " pdb=" CA GLY C 279 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 15955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3816 0.101 - 0.203: 164 0.203 - 0.304: 13 0.304 - 0.406: 4 0.406 - 0.507: 1 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA ARG B 432 " pdb=" N ARG B 432 " pdb=" C ARG B 432 " pdb=" CB ARG B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CA THR D 682 " pdb=" N THR D 682 " pdb=" C THR D 682 " pdb=" CB THR D 682 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C10 4KZ E 801 " pdb=" C11 4KZ E 801 " pdb=" C18 4KZ E 801 " pdb=" N9 4KZ E 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 3995 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 589 " -0.189 2.00e-02 2.50e+03 2.74e-01 7.52e+02 pdb=" C GLU F 589 " 0.446 2.00e-02 2.50e+03 pdb=" O GLU F 589 " -0.256 2.00e-02 2.50e+03 pdb=" N THR F 590 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ D 802 " 0.206 2.00e-02 2.50e+03 2.22e-01 6.19e+02 pdb=" C18 4KZ D 802 " -0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ D 802 " 0.264 2.00e-02 2.50e+03 pdb=" N20 4KZ D 802 " -0.341 2.00e-02 2.50e+03 pdb=" O19 4KZ D 802 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ B 802 " -0.200 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" C18 4KZ B 802 " 0.127 2.00e-02 2.50e+03 pdb=" C21 4KZ B 802 " -0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ B 802 " 0.329 2.00e-02 2.50e+03 pdb=" O19 4KZ B 802 " 0.001 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 17 1.97 - 2.70: 1256 2.70 - 3.44: 38194 3.44 - 4.17: 59650 4.17 - 4.90: 105580 Nonbonded interactions: 204697 Sorted by model distance: nonbonded pdb=" NH1 ARG A 385 " pdb=" O GLY B 433 " model vdw 1.240 3.120 nonbonded pdb=" CZ ARG A 385 " pdb=" CA GLY B 433 " model vdw 1.414 3.670 nonbonded pdb=" O VAL C 667 " pdb=" NZ LYS C 674 " model vdw 1.463 3.120 nonbonded pdb=" NH1 ARG A 385 " pdb=" C GLY B 433 " model vdw 1.502 3.350 nonbonded pdb=" CB VAL B 352 " pdb=" CE MET B 485 " model vdw 1.586 3.890 ... (remaining 204692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 244 through 780) selection = (chain 'B' and resid 244 through 780) selection = (chain 'C' and resid 244 through 780) selection = (chain 'D' and resid 244 through 780) selection = (chain 'E' and resid 244 through 780) selection = (chain 'F' and resid 244 through 780) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.010 Find NCS groups from input model: 0.740 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.015 1.643 25969 Z= 1.167 Angle : 0.981 73.933 35219 Z= 0.611 Chirality : 0.050 0.507 3998 Planarity : 0.009 0.274 4542 Dihedral : 15.772 155.990 10018 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.97 % Favored : 91.87 % Rotamer: Outliers : 0.56 % Allowed : 7.33 % Favored : 92.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.13), residues: 3199 helix: -3.27 (0.11), residues: 1190 sheet: -1.70 (0.24), residues: 428 loop : -2.54 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 336 TYR 0.019 0.001 TYR E 455 PHE 0.017 0.002 PHE C 657 TRP 0.035 0.002 TRP A 431 HIS 0.004 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.01314 / 0.98 (25961) covalent geometry : angle 0.98110 / 0.61 (35219) hydrogen bonds : bond 0.29085 / 18.93 ( 890) hydrogen bonds : angle 10.07394 / 7.15 ( 2499) Misc. bond : bond 0.36344 / 18.18 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 437 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 ASN cc_start: 0.8857 (m-40) cc_final: 0.8564 (p0) REVERT: A 431 TRP cc_start: 0.7201 (t60) cc_final: 0.6935 (t60) REVERT: A 439 MET cc_start: 0.9353 (mmm) cc_final: 0.8705 (mmm) REVERT: B 439 MET cc_start: 0.9349 (mmm) cc_final: 0.8951 (mmm) REVERT: B 472 ASN cc_start: 0.8709 (p0) cc_final: 0.8424 (p0) REVERT: B 495 ASN cc_start: 0.9164 (m-40) cc_final: 0.8879 (m-40) REVERT: B 659 ASN cc_start: 0.8927 (t0) cc_final: 0.8640 (t0) REVERT: B 662 ASP cc_start: 0.7891 (m-30) cc_final: 0.7546 (m-30) REVERT: B 675 ASP cc_start: 0.8246 (t0) cc_final: 0.7998 (t0) REVERT: C 317 GLU cc_start: 0.7935 (pt0) cc_final: 0.7580 (pt0) REVERT: C 546 GLU cc_start: 0.8437 (mp0) cc_final: 0.8058 (mp0) REVERT: C 584 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7364 (ttm110) REVERT: F 376 PHE cc_start: 0.5342 (t80) cc_final: 0.4636 (t80) REVERT: F 698 MET cc_start: 0.7925 (mmm) cc_final: 0.7202 (mmm) REVERT: D 265 LYS cc_start: 0.8399 (tptp) cc_final: 0.8121 (tppt) REVERT: D 276 MET cc_start: 0.6174 (tmm) cc_final: 0.5929 (tmm) REVERT: D 479 ARG cc_start: 0.8400 (mmt-90) cc_final: 0.8199 (mmm160) REVERT: D 596 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8915 (m) REVERT: D 683 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8358 (mpt) REVERT: D 738 ASP cc_start: 0.8330 (t0) cc_final: 0.7198 (t0) REVERT: D 776 MET cc_start: 0.3785 (mtp) cc_final: 0.3443 (mpp) REVERT: E 368 ILE cc_start: 0.8765 (mm) cc_final: 0.8427 (mm) REVERT: E 409 MET cc_start: 0.7482 (mmt) cc_final: 0.7191 (mmm) REVERT: E 497 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8372 (mt-10) REVERT: E 516 MET cc_start: 0.8382 (mmm) cc_final: 0.7332 (mtp) outliers start: 15 outliers final: 5 residues processed: 449 average time/residue: 0.1996 time to fit residues: 136.7400 Evaluate side-chains 307 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 300 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 683 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0010 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN B 340 GLN B 393 HIS B 510 GLN B 638 GLN C 739 ASN F 278 GLN F 340 GLN F 373 ASN F 449 ASN F 739 ASN D 373 ASN D 411 GLN D 454 HIS D 495 ASN D 504 GLN D 510 GLN D 598 GLN D 628 GLN E 277 GLN E 393 HIS E 411 GLN E 447 GLN E 504 GLN E 510 GLN E 593 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.119690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095428 restraints weight = 66854.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098000 restraints weight = 32042.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099647 restraints weight = 19581.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100723 restraints weight = 14049.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101362 restraints weight = 11237.190| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 25969 Z= 0.157 Angle : 0.692 9.643 35219 Z= 0.347 Chirality : 0.046 0.194 3998 Planarity : 0.006 0.051 4542 Dihedral : 9.507 152.601 3729 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 2.16 % Allowed : 12.16 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.14), residues: 3201 helix: -1.66 (0.13), residues: 1272 sheet: -0.96 (0.25), residues: 420 loop : -2.09 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 336 TYR 0.018 0.001 TYR E 455 PHE 0.018 0.002 PHE D 376 TRP 0.021 0.001 TRP A 602 HIS 0.005 0.001 HIS F 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (25961) covalent geometry : angle 0.69232 / 0.35 (35219) hydrogen bonds : bond 0.05277 / 3.47 ( 890) hydrogen bonds : angle 6.28079 / 4.42 ( 2499) Misc. bond : bond 0.00421 / 0.21 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.4154 (tmm) cc_final: 0.2783 (mmp) REVERT: A 331 GLU cc_start: 0.8712 (pt0) cc_final: 0.8359 (pt0) REVERT: A 372 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8056 (mtp) REVERT: A 373 ASN cc_start: 0.8811 (m-40) cc_final: 0.8469 (p0) REVERT: A 439 MET cc_start: 0.9251 (mmm) cc_final: 0.8560 (mmm) REVERT: B 252 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8814 (tptt) REVERT: B 439 MET cc_start: 0.9105 (mmm) cc_final: 0.8667 (mmm) REVERT: B 472 ASN cc_start: 0.8698 (p0) cc_final: 0.8463 (p0) REVERT: B 495 ASN cc_start: 0.9028 (m-40) cc_final: 0.8779 (m-40) REVERT: B 602 TRP cc_start: 0.8718 (t60) cc_final: 0.8500 (t60) REVERT: B 659 ASN cc_start: 0.8840 (t0) cc_final: 0.8492 (t0) REVERT: B 662 ASP cc_start: 0.7846 (m-30) cc_final: 0.7598 (m-30) REVERT: C 276 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7980 (ttp) REVERT: C 426 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8534 (mmtm) REVERT: C 533 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 546 GLU cc_start: 0.8241 (mp0) cc_final: 0.7902 (mp0) REVERT: C 739 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.9028 (m-40) REVERT: F 376 PHE cc_start: 0.5492 (t80) cc_final: 0.4830 (t80) REVERT: F 598 GLN cc_start: 0.7655 (mm110) cc_final: 0.7369 (mm110) REVERT: F 633 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: F 698 MET cc_start: 0.7875 (mmm) cc_final: 0.7175 (mmm) REVERT: D 265 LYS cc_start: 0.8266 (tptp) cc_final: 0.8006 (tppt) REVERT: D 391 ARG cc_start: 0.8358 (mtm180) cc_final: 0.8062 (mtm180) REVERT: D 444 ASP cc_start: 0.8714 (t0) cc_final: 0.8374 (t0) REVERT: D 495 ASN cc_start: 0.9229 (m110) cc_final: 0.8984 (m110) REVERT: D 596 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8981 (m) REVERT: D 675 ASP cc_start: 0.8560 (t0) cc_final: 0.8269 (t0) REVERT: D 683 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7890 (mpt) REVERT: D 738 ASP cc_start: 0.8318 (t0) cc_final: 0.7936 (t0) REVERT: D 776 MET cc_start: 0.3819 (mtp) cc_final: 0.3615 (mpp) REVERT: E 409 MET cc_start: 0.7427 (mmt) cc_final: 0.7126 (mmm) REVERT: E 516 MET cc_start: 0.8463 (mmm) cc_final: 0.7201 (mtp) REVERT: E 703 THR cc_start: 0.9328 (p) cc_final: 0.9056 (p) outliers start: 58 outliers final: 31 residues processed: 421 average time/residue: 0.1746 time to fit residues: 117.1741 Evaluate side-chains 348 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 739 ASN Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 163 optimal weight: 20.0000 chunk 253 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 117 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN C 447 GLN C 510 GLN C 739 ASN F 407 HIS F 495 ASN F 727 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.119350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094894 restraints weight = 67489.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.097477 restraints weight = 32373.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099051 restraints weight = 19767.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100096 restraints weight = 14245.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100729 restraints weight = 11456.019| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25969 Z= 0.168 Angle : 0.659 9.600 35219 Z= 0.324 Chirality : 0.045 0.250 3998 Planarity : 0.005 0.055 4542 Dihedral : 8.926 157.016 3720 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.16 % Allowed : 14.39 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.14), residues: 3201 helix: -1.17 (0.14), residues: 1278 sheet: -0.67 (0.26), residues: 409 loop : -1.92 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 336 TYR 0.014 0.001 TYR E 289 PHE 0.018 0.002 PHE D 376 TRP 0.020 0.001 TRP D 602 HIS 0.004 0.001 HIS C 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (25961) covalent geometry : angle 0.65903 / 0.32 (35219) hydrogen bonds : bond 0.04297 / 2.85 ( 890) hydrogen bonds : angle 5.68166 / 3.98 ( 2499) Misc. bond : bond 0.00189 / 0.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 333 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3517 (tmm) cc_final: 0.2886 (mmp) REVERT: A 431 TRP cc_start: 0.7223 (t60) cc_final: 0.7020 (t60) REVERT: B 252 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8816 (tptt) REVERT: B 258 MET cc_start: 0.8166 (mtp) cc_final: 0.7924 (mtp) REVERT: B 439 MET cc_start: 0.9131 (mmm) cc_final: 0.8722 (mmm) REVERT: B 495 ASN cc_start: 0.9066 (m-40) cc_final: 0.8796 (m-40) REVERT: B 602 TRP cc_start: 0.8743 (t60) cc_final: 0.8500 (t60) REVERT: B 659 ASN cc_start: 0.8893 (t0) cc_final: 0.8530 (t0) REVERT: B 662 ASP cc_start: 0.7869 (m-30) cc_final: 0.7614 (m-30) REVERT: C 432 ARG cc_start: 0.7094 (tpt170) cc_final: 0.6639 (tpm170) REVERT: C 533 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 546 GLU cc_start: 0.8380 (mp0) cc_final: 0.7824 (mp0) REVERT: F 376 PHE cc_start: 0.5570 (t80) cc_final: 0.4962 (t80) REVERT: F 427 MET cc_start: 0.2774 (tpp) cc_final: 0.1814 (tpp) REVERT: F 439 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7180 (mpp) REVERT: F 598 GLN cc_start: 0.7730 (mm110) cc_final: 0.7263 (mm110) REVERT: F 633 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8035 (mtp) REVERT: F 698 MET cc_start: 0.7872 (mmm) cc_final: 0.7236 (mmm) REVERT: F 713 MET cc_start: 0.8905 (mmm) cc_final: 0.8690 (mmm) REVERT: D 265 LYS cc_start: 0.8287 (tptp) cc_final: 0.7994 (tppt) REVERT: D 276 MET cc_start: 0.6625 (tmm) cc_final: 0.6200 (tmm) REVERT: D 292 TRP cc_start: 0.8427 (m100) cc_final: 0.8174 (m-90) REVERT: D 455 TYR cc_start: 0.8629 (t80) cc_final: 0.8338 (t80) REVERT: D 495 ASN cc_start: 0.9236 (m110) cc_final: 0.8865 (t0) REVERT: D 513 GLU cc_start: 0.8502 (tp30) cc_final: 0.8231 (tp30) REVERT: D 596 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9011 (m) REVERT: D 738 ASP cc_start: 0.8297 (t0) cc_final: 0.8087 (t0) REVERT: D 776 MET cc_start: 0.3889 (mtp) cc_final: 0.3611 (mpp) REVERT: E 409 MET cc_start: 0.7538 (mmt) cc_final: 0.7212 (mmm) REVERT: E 485 MET cc_start: 0.6579 (tmm) cc_final: 0.6252 (tmm) REVERT: E 503 ARG cc_start: 0.8169 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: E 516 MET cc_start: 0.8458 (mmm) cc_final: 0.7262 (mtp) REVERT: E 703 THR cc_start: 0.9372 (p) cc_final: 0.9090 (p) outliers start: 85 outliers final: 48 residues processed: 387 average time/residue: 0.1629 time to fit residues: 102.9369 Evaluate side-chains 355 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 218 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 176 optimal weight: 40.0000 chunk 137 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN C 666 HIS F 495 ASN F 510 GLN ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.114635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090938 restraints weight = 67976.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093400 restraints weight = 32965.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094961 restraints weight = 20230.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096012 restraints weight = 14642.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096684 restraints weight = 11707.748| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25969 Z= 0.204 Angle : 0.673 9.033 35219 Z= 0.328 Chirality : 0.045 0.270 3998 Planarity : 0.005 0.051 4542 Dihedral : 8.516 157.493 3717 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.24 % Allowed : 15.69 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 3201 helix: -0.92 (0.14), residues: 1285 sheet: -0.54 (0.27), residues: 397 loop : -1.85 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 709 TYR 0.016 0.001 TYR E 289 PHE 0.018 0.002 PHE D 376 TRP 0.020 0.001 TRP D 602 HIS 0.005 0.001 HIS C 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (25961) covalent geometry : angle 0.67278 / 0.33 (35219) hydrogen bonds : bond 0.03863 / 2.54 ( 890) hydrogen bonds : angle 5.47142 / 3.83 ( 2499) Misc. bond : bond 0.00113 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 320 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3486 (tmm) cc_final: 0.2561 (mmm) REVERT: A 439 MET cc_start: 0.9142 (mmm) cc_final: 0.8635 (mmm) REVERT: B 252 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8823 (tptt) REVERT: B 258 MET cc_start: 0.8163 (mtp) cc_final: 0.7849 (mtp) REVERT: B 439 MET cc_start: 0.9153 (mmm) cc_final: 0.8741 (mmm) REVERT: B 495 ASN cc_start: 0.9046 (m-40) cc_final: 0.8772 (m-40) REVERT: B 659 ASN cc_start: 0.8925 (t0) cc_final: 0.8542 (t0) REVERT: B 662 ASP cc_start: 0.7872 (m-30) cc_final: 0.7599 (m-30) REVERT: B 698 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: C 533 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7984 (mt-10) REVERT: C 546 GLU cc_start: 0.8379 (mp0) cc_final: 0.7783 (mp0) REVERT: F 376 PHE cc_start: 0.5652 (t80) cc_final: 0.4965 (t80) REVERT: F 427 MET cc_start: 0.2838 (tpp) cc_final: 0.2394 (tpp) REVERT: F 598 GLN cc_start: 0.7772 (mm110) cc_final: 0.7368 (mm110) REVERT: F 633 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: F 698 MET cc_start: 0.7848 (mmm) cc_final: 0.7267 (mmm) REVERT: D 265 LYS cc_start: 0.8327 (tptp) cc_final: 0.8013 (tppt) REVERT: D 495 ASN cc_start: 0.9261 (m110) cc_final: 0.8855 (t0) REVERT: D 596 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9044 (m) REVERT: D 738 ASP cc_start: 0.8362 (t0) cc_final: 0.8078 (t0) REVERT: D 776 MET cc_start: 0.3989 (mtp) cc_final: 0.3699 (mpp) REVERT: E 373 ASN cc_start: 0.8567 (t0) cc_final: 0.8356 (t0) REVERT: E 409 MET cc_start: 0.7539 (mmt) cc_final: 0.7074 (tpp) REVERT: E 503 ARG cc_start: 0.8166 (tmm-80) cc_final: 0.7703 (tmm-80) REVERT: E 516 MET cc_start: 0.8501 (mmm) cc_final: 0.7356 (mtp) REVERT: E 703 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9150 (p) outliers start: 87 outliers final: 61 residues processed: 375 average time/residue: 0.1620 time to fit residues: 99.8035 Evaluate side-chains 358 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 628 GLN Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 727 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 23 optimal weight: 0.0020 chunk 245 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 315 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 495 ASN ** E 739 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 = 0.3863 r_free = 0.3863 target = 0.120244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095922 restraints weight = 66951.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098448 restraints weight = 32198.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100076 restraints weight = 19702.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101141 restraints weight = 14165.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101842 restraints weight = 11350.366| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25969 Z= 0.125 Angle : 0.620 10.001 35219 Z= 0.302 Chirality : 0.044 0.273 3998 Planarity : 0.005 0.051 4542 Dihedral : 8.038 156.796 3717 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.57 % Allowed : 16.70 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3201 helix: -0.59 (0.14), residues: 1289 sheet: -0.45 (0.27), residues: 399 loop : -1.66 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 432 TYR 0.012 0.001 TYR D 455 PHE 0.022 0.001 PHE D 376 TRP 0.023 0.001 TRP D 602 HIS 0.004 0.001 HIS C 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (25961) covalent geometry : angle 0.61961 / 0.30 (35219) hydrogen bonds : bond 0.03337 / 2.18 ( 890) hydrogen bonds : angle 5.14532 / 3.59 ( 2499) Misc. bond : bond 0.00087 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 341 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3400 (tmm) cc_final: 0.2629 (mmp) REVERT: A 375 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8672 (mtpp) REVERT: A 439 MET cc_start: 0.9112 (mmm) cc_final: 0.8591 (mmm) REVERT: B 252 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8796 (tptt) REVERT: B 258 MET cc_start: 0.8089 (mtp) cc_final: 0.7735 (mtp) REVERT: B 331 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 439 MET cc_start: 0.9093 (mmm) cc_final: 0.8619 (mmm) REVERT: B 602 TRP cc_start: 0.8835 (t60) cc_final: 0.8617 (t60) REVERT: B 626 THR cc_start: 0.8907 (p) cc_final: 0.8702 (p) REVERT: B 659 ASN cc_start: 0.8891 (t0) cc_final: 0.8512 (t0) REVERT: B 662 ASP cc_start: 0.7791 (m-30) cc_final: 0.7514 (m-30) REVERT: B 698 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7447 (mtp) REVERT: B 735 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9209 (mp) REVERT: C 389 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 469 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 516 MET cc_start: 0.8035 (mmm) cc_final: 0.7700 (mmm) REVERT: C 546 GLU cc_start: 0.8371 (mp0) cc_final: 0.7777 (mp0) REVERT: F 409 MET cc_start: 0.6771 (tpt) cc_final: 0.6492 (tpt) REVERT: F 427 MET cc_start: 0.2831 (tpp) cc_final: 0.1881 (tpp) REVERT: F 598 GLN cc_start: 0.7743 (mm110) cc_final: 0.7321 (mm110) REVERT: F 633 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: F 698 MET cc_start: 0.7706 (mmm) cc_final: 0.7104 (mmm) REVERT: D 265 LYS cc_start: 0.8205 (tptp) cc_final: 0.7886 (tppt) REVERT: D 455 TYR cc_start: 0.8615 (t80) cc_final: 0.8399 (t80) REVERT: D 495 ASN cc_start: 0.9274 (m110) cc_final: 0.8725 (t0) REVERT: D 496 MET cc_start: 0.9042 (pmm) cc_final: 0.8642 (tpt) REVERT: D 596 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8991 (m) REVERT: D 738 ASP cc_start: 0.8343 (t0) cc_final: 0.8059 (t0) REVERT: D 776 MET cc_start: 0.3907 (mtp) cc_final: 0.3627 (mpp) REVERT: E 373 ASN cc_start: 0.8634 (t0) cc_final: 0.8401 (t0) REVERT: E 498 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.6226 (mptt) REVERT: E 516 MET cc_start: 0.8412 (mmm) cc_final: 0.7340 (mtp) outliers start: 96 outliers final: 56 residues processed: 409 average time/residue: 0.1649 time to fit residues: 110.2027 Evaluate side-chains 369 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 306 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 232 optimal weight: 0.9990 chunk 268 optimal weight: 0.4980 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 159 optimal weight: 40.0000 chunk 304 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 309 ASN F 495 ASN D 377 HIS ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.115790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091949 restraints weight = 67847.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094395 restraints weight = 32859.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095975 restraints weight = 20186.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097010 restraints weight = 14595.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097668 restraints weight = 11749.558| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25969 Z= 0.169 Angle : 0.650 9.918 35219 Z= 0.314 Chirality : 0.044 0.266 3998 Planarity : 0.005 0.055 4542 Dihedral : 7.927 158.231 3717 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 18.63 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 3201 helix: -0.40 (0.14), residues: 1293 sheet: -0.42 (0.27), residues: 399 loop : -1.57 (0.17), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 336 TYR 0.013 0.001 TYR E 289 PHE 0.023 0.002 PHE D 376 TRP 0.025 0.001 TRP D 602 HIS 0.005 0.001 HIS C 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (25961) covalent geometry : angle 0.65028 / 0.31 (35219) hydrogen bonds : bond 0.03318 / 2.17 ( 890) hydrogen bonds : angle 5.06309 / 3.52 ( 2499) Misc. bond : bond 0.00103 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 320 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3357 (tmm) cc_final: 0.2591 (mmm) REVERT: A 385 ARG cc_start: 0.7220 (ppt170) cc_final: 0.6870 (ptt90) REVERT: A 439 MET cc_start: 0.9170 (mmm) cc_final: 0.8641 (mmm) REVERT: B 252 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8826 (tptt) REVERT: B 258 MET cc_start: 0.8130 (mtp) cc_final: 0.7765 (mtp) REVERT: B 269 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8134 (mm-30) REVERT: B 331 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 439 MET cc_start: 0.9163 (mmm) cc_final: 0.8694 (mmm) REVERT: B 602 TRP cc_start: 0.8868 (t60) cc_final: 0.8652 (t60) REVERT: B 626 THR cc_start: 0.8924 (p) cc_final: 0.8693 (p) REVERT: B 659 ASN cc_start: 0.8926 (t0) cc_final: 0.8550 (t0) REVERT: B 662 ASP cc_start: 0.7823 (m-30) cc_final: 0.7533 (m-30) REVERT: B 698 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7489 (mtp) REVERT: B 735 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9197 (mp) REVERT: C 282 GLU cc_start: 0.8655 (pm20) cc_final: 0.8180 (pp20) REVERT: C 469 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8937 (p) REVERT: C 533 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7996 (pt0) REVERT: C 546 GLU cc_start: 0.8393 (mp0) cc_final: 0.7818 (mp0) REVERT: C 675 ASP cc_start: 0.7944 (t0) cc_final: 0.7376 (p0) REVERT: F 427 MET cc_start: 0.2820 (tpp) cc_final: 0.1863 (tpp) REVERT: F 598 GLN cc_start: 0.7821 (mm110) cc_final: 0.7378 (mm110) REVERT: F 633 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7998 (mtp) REVERT: F 698 MET cc_start: 0.7752 (mmm) cc_final: 0.7182 (mmm) REVERT: D 276 MET cc_start: 0.6646 (tmm) cc_final: 0.6279 (tmm) REVERT: D 455 TYR cc_start: 0.8772 (t80) cc_final: 0.8542 (t80) REVERT: D 495 ASN cc_start: 0.9289 (m110) cc_final: 0.8857 (t0) REVERT: D 596 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9014 (m) REVERT: D 738 ASP cc_start: 0.8411 (t0) cc_final: 0.8139 (t0) REVERT: D 776 MET cc_start: 0.4007 (mtp) cc_final: 0.3669 (mpp) REVERT: E 373 ASN cc_start: 0.8648 (t0) cc_final: 0.8383 (t0) REVERT: E 409 MET cc_start: 0.7374 (mmt) cc_final: 0.7105 (mmm) REVERT: E 702 MET cc_start: 0.8830 (ptp) cc_final: 0.8106 (ptp) outliers start: 87 outliers final: 67 residues processed: 375 average time/residue: 0.1650 time to fit residues: 101.3358 Evaluate side-chains 378 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 306 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 628 GLN Chi-restraints excluded: chain F residue 633 MET Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 52 optimal weight: 9.9990 chunk 287 optimal weight: 30.0000 chunk 301 optimal weight: 0.0170 chunk 236 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 309 ASN F 449 ASN F 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.119240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095480 restraints weight = 66639.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098054 restraints weight = 31999.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099624 restraints weight = 19468.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100666 restraints weight = 13978.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101348 restraints weight = 11222.029| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25969 Z= 0.105 Angle : 0.613 12.324 35219 Z= 0.294 Chirality : 0.043 0.266 3998 Planarity : 0.005 0.052 4542 Dihedral : 7.542 156.929 3717 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 19.04 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3201 helix: -0.09 (0.15), residues: 1290 sheet: -0.32 (0.26), residues: 400 loop : -1.46 (0.17), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 432 TYR 0.010 0.001 TYR A 643 PHE 0.030 0.001 PHE D 376 TRP 0.030 0.001 TRP D 602 HIS 0.003 0.001 HIS F 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (25961) covalent geometry : angle 0.61348 / 0.29 (35219) hydrogen bonds : bond 0.02898 / 1.90 ( 890) hydrogen bonds : angle 4.74536 / 3.29 ( 2499) Misc. bond : bond 0.00114 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 370 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3146 (tmm) cc_final: 0.2460 (mmm) REVERT: A 331 GLU cc_start: 0.8540 (pt0) cc_final: 0.8190 (pt0) REVERT: A 375 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8643 (mtpp) REVERT: A 385 ARG cc_start: 0.7223 (ppt170) cc_final: 0.6683 (ptt-90) REVERT: A 439 MET cc_start: 0.9130 (mmm) cc_final: 0.8621 (mmm) REVERT: B 252 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8784 (tptt) REVERT: B 258 MET cc_start: 0.7953 (mtp) cc_final: 0.7618 (mtp) REVERT: B 422 ASP cc_start: 0.8137 (t0) cc_final: 0.7280 (p0) REVERT: B 439 MET cc_start: 0.9133 (mmm) cc_final: 0.8599 (mmm) REVERT: B 626 THR cc_start: 0.8808 (p) cc_final: 0.8582 (p) REVERT: B 659 ASN cc_start: 0.8822 (t0) cc_final: 0.8475 (t0) REVERT: B 698 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7293 (mtp) REVERT: B 735 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9132 (mp) REVERT: C 276 MET cc_start: 0.8265 (tmm) cc_final: 0.7870 (ptm) REVERT: C 282 GLU cc_start: 0.8696 (pm20) cc_final: 0.8395 (pm20) REVERT: C 533 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7907 (pt0) REVERT: C 546 GLU cc_start: 0.8418 (mp0) cc_final: 0.7865 (mp0) REVERT: C 583 TYR cc_start: 0.8754 (m-80) cc_final: 0.8486 (m-80) REVERT: C 675 ASP cc_start: 0.7854 (t0) cc_final: 0.7363 (p0) REVERT: F 273 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6823 (tt) REVERT: F 427 MET cc_start: 0.2856 (tpp) cc_final: 0.1968 (tpp) REVERT: F 598 GLN cc_start: 0.7728 (mm110) cc_final: 0.7217 (mm110) REVERT: F 660 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8720 (mtpp) REVERT: F 698 MET cc_start: 0.7623 (mmm) cc_final: 0.7056 (mmm) REVERT: D 391 ARG cc_start: 0.8410 (mtm180) cc_final: 0.8165 (ptm160) REVERT: D 495 ASN cc_start: 0.9246 (m110) cc_final: 0.8830 (t0) REVERT: D 596 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8941 (m) REVERT: D 738 ASP cc_start: 0.8354 (t0) cc_final: 0.8098 (t0) REVERT: D 776 MET cc_start: 0.3982 (mtp) cc_final: 0.3674 (mpp) REVERT: E 373 ASN cc_start: 0.8698 (t0) cc_final: 0.8413 (t0) REVERT: E 498 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.6681 (mmmt) REVERT: E 702 MET cc_start: 0.8720 (ptp) cc_final: 0.8055 (ptp) outliers start: 79 outliers final: 52 residues processed: 420 average time/residue: 0.1672 time to fit residues: 113.8793 Evaluate side-chains 392 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 194 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 280 optimal weight: 8.9990 chunk 293 optimal weight: 0.7980 chunk 162 optimal weight: 0.3980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN F 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093314 restraints weight = 67492.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095870 restraints weight = 32589.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097403 restraints weight = 19906.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098453 restraints weight = 14398.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099124 restraints weight = 11592.037| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25969 Z= 0.147 Angle : 0.638 10.155 35219 Z= 0.308 Chirality : 0.044 0.308 3998 Planarity : 0.005 0.052 4542 Dihedral : 7.573 159.298 3717 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.12 % Allowed : 19.67 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3201 helix: 0.02 (0.15), residues: 1298 sheet: -0.19 (0.27), residues: 396 loop : -1.41 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 709 TYR 0.030 0.001 TYR D 455 PHE 0.033 0.002 PHE D 376 TRP 0.039 0.001 TRP D 507 HIS 0.004 0.001 HIS C 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (25961) covalent geometry : angle 0.63827 / 0.31 (35219) hydrogen bonds : bond 0.02978 / 1.94 ( 890) hydrogen bonds : angle 4.78244 / 3.33 ( 2499) Misc. bond : bond 0.00085 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.3070 (tmm) cc_final: 0.2651 (mmm) REVERT: A 375 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: A 385 ARG cc_start: 0.7348 (ppt170) cc_final: 0.6808 (ptt-90) REVERT: A 439 MET cc_start: 0.9182 (mmm) cc_final: 0.8672 (mmm) REVERT: B 252 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8799 (tptt) REVERT: B 258 MET cc_start: 0.8001 (mtp) cc_final: 0.7679 (mtp) REVERT: B 385 ARG cc_start: 0.7773 (ptt90) cc_final: 0.7550 (ptm-80) REVERT: B 422 ASP cc_start: 0.7615 (t0) cc_final: 0.7375 (p0) REVERT: B 439 MET cc_start: 0.9199 (mmm) cc_final: 0.8716 (mmm) REVERT: B 626 THR cc_start: 0.8816 (p) cc_final: 0.8598 (p) REVERT: B 659 ASN cc_start: 0.8886 (t0) cc_final: 0.8507 (t0) REVERT: B 698 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7374 (mtp) REVERT: B 735 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9119 (mp) REVERT: C 276 MET cc_start: 0.8298 (tmm) cc_final: 0.7962 (ptm) REVERT: C 533 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7958 (pt0) REVERT: C 546 GLU cc_start: 0.8423 (mp0) cc_final: 0.7860 (mp0) REVERT: C 626 THR cc_start: 0.8913 (p) cc_final: 0.8577 (p) REVERT: C 675 ASP cc_start: 0.7937 (t0) cc_final: 0.7398 (p0) REVERT: F 273 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7067 (tt) REVERT: F 276 MET cc_start: -0.1229 (mmm) cc_final: -0.3398 (ttm) REVERT: F 427 MET cc_start: 0.2877 (tpp) cc_final: 0.1966 (tpp) REVERT: F 598 GLN cc_start: 0.7808 (mm110) cc_final: 0.7295 (mm110) REVERT: F 698 MET cc_start: 0.7684 (mmm) cc_final: 0.7117 (mmm) REVERT: D 372 MET cc_start: 0.7987 (tmm) cc_final: 0.7727 (tmm) REVERT: D 391 ARG cc_start: 0.8423 (mtm180) cc_final: 0.8165 (ptm160) REVERT: D 495 ASN cc_start: 0.9293 (m110) cc_final: 0.8879 (t0) REVERT: D 660 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8355 (mmmm) REVERT: D 738 ASP cc_start: 0.8420 (t0) cc_final: 0.8158 (t0) REVERT: D 776 MET cc_start: 0.4049 (mtp) cc_final: 0.3695 (mpp) REVERT: E 373 ASN cc_start: 0.8719 (t0) cc_final: 0.8437 (t0) REVERT: E 439 MET cc_start: 0.8402 (mpp) cc_final: 0.7880 (mpp) REVERT: E 498 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6744 (mmmt) REVERT: E 702 MET cc_start: 0.8748 (ptp) cc_final: 0.8056 (ptp) outliers start: 84 outliers final: 59 residues processed: 388 average time/residue: 0.1598 time to fit residues: 101.8428 Evaluate side-chains 378 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 131 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 278 optimal weight: 30.0000 chunk 117 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 309 ASN F 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.118170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094262 restraints weight = 67407.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096835 restraints weight = 32072.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098512 restraints weight = 19341.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099585 restraints weight = 13747.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100242 restraints weight = 10972.573| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25969 Z= 0.118 Angle : 0.635 12.971 35219 Z= 0.304 Chirality : 0.044 0.321 3998 Planarity : 0.005 0.052 4542 Dihedral : 7.439 158.204 3716 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.94 % Allowed : 20.38 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3201 helix: 0.10 (0.15), residues: 1299 sheet: -0.21 (0.26), residues: 409 loop : -1.34 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 385 TYR 0.010 0.001 TYR A 493 PHE 0.030 0.001 PHE D 376 TRP 0.030 0.001 TRP D 602 HIS 0.004 0.001 HIS F 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (25961) covalent geometry : angle 0.63541 / 0.30 (35219) hydrogen bonds : bond 0.02881 / 1.88 ( 890) hydrogen bonds : angle 4.69017 / 3.25 ( 2499) Misc. bond : bond 0.00086 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 333 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LYS cc_start: 0.7638 (tptp) cc_final: 0.7291 (tttt) REVERT: A 276 MET cc_start: 0.3179 (tmm) cc_final: 0.2725 (mmm) REVERT: A 375 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: A 385 ARG cc_start: 0.7354 (ppt170) cc_final: 0.6863 (ptt-90) REVERT: A 439 MET cc_start: 0.9133 (mmm) cc_final: 0.8656 (mmm) REVERT: B 252 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8792 (tptt) REVERT: B 258 MET cc_start: 0.7956 (mtp) cc_final: 0.7650 (mtp) REVERT: B 385 ARG cc_start: 0.7750 (ptt90) cc_final: 0.7495 (ptm-80) REVERT: B 386 ASP cc_start: 0.8375 (p0) cc_final: 0.7928 (t70) REVERT: B 439 MET cc_start: 0.9178 (mmm) cc_final: 0.8694 (mmm) REVERT: B 626 THR cc_start: 0.8752 (p) cc_final: 0.8536 (p) REVERT: B 659 ASN cc_start: 0.8854 (t0) cc_final: 0.8479 (t0) REVERT: B 698 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7292 (mtp) REVERT: B 735 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9104 (mp) REVERT: C 276 MET cc_start: 0.8266 (tmm) cc_final: 0.8010 (ptm) REVERT: C 385 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7543 (tpp-160) REVERT: C 533 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7856 (pt0) REVERT: C 626 THR cc_start: 0.8887 (p) cc_final: 0.8578 (p) REVERT: C 675 ASP cc_start: 0.7913 (t0) cc_final: 0.7385 (p0) REVERT: C 715 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7722 (tp) REVERT: F 273 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7054 (tt) REVERT: F 276 MET cc_start: -0.1217 (mmm) cc_final: -0.3339 (ttm) REVERT: F 427 MET cc_start: 0.2791 (tpp) cc_final: 0.1906 (tpp) REVERT: F 598 GLN cc_start: 0.7752 (mm110) cc_final: 0.7224 (mm110) REVERT: F 698 MET cc_start: 0.7649 (mmm) cc_final: 0.7073 (mmm) REVERT: D 391 ARG cc_start: 0.8426 (mtm180) cc_final: 0.8195 (ptm160) REVERT: D 495 ASN cc_start: 0.9280 (m110) cc_final: 0.8858 (t0) REVERT: D 738 ASP cc_start: 0.8393 (t0) cc_final: 0.8140 (t0) REVERT: D 776 MET cc_start: 0.4071 (mtp) cc_final: 0.3729 (mpp) REVERT: E 373 ASN cc_start: 0.8716 (t0) cc_final: 0.8435 (t0) REVERT: E 409 MET cc_start: 0.7253 (mmt) cc_final: 0.6919 (mmm) REVERT: E 439 MET cc_start: 0.8370 (mpp) cc_final: 0.7860 (mpp) REVERT: E 498 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6722 (mmmt) outliers start: 79 outliers final: 60 residues processed: 382 average time/residue: 0.1637 time to fit residues: 101.9067 Evaluate side-chains 391 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 628 GLN Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 53 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 305 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 52 optimal weight: 0.0010 chunk 135 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 309 ASN F 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094959 restraints weight = 67197.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.097468 restraints weight = 32134.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099078 restraints weight = 19522.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100067 restraints weight = 13963.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100790 restraints weight = 11277.506| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25969 Z= 0.120 Angle : 0.637 12.980 35219 Z= 0.305 Chirality : 0.044 0.320 3998 Planarity : 0.005 0.051 4542 Dihedral : 7.372 158.698 3716 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.57 % Allowed : 20.83 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3201 helix: 0.15 (0.15), residues: 1305 sheet: -0.22 (0.26), residues: 414 loop : -1.33 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 709 TYR 0.010 0.001 TYR A 493 PHE 0.030 0.001 PHE D 376 TRP 0.034 0.001 TRP D 602 HIS 0.016 0.001 HIS F 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (25961) covalent geometry : angle 0.63655 / 0.31 (35219) hydrogen bonds : bond 0.02914 / 1.91 ( 890) hydrogen bonds : angle 4.64258 / 3.22 ( 2499) Misc. bond : bond 0.00084 / 0.05 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LYS cc_start: 0.7632 (tptp) cc_final: 0.7301 (tttt) REVERT: A 276 MET cc_start: 0.3153 (tmm) cc_final: 0.2667 (mmm) REVERT: A 385 ARG cc_start: 0.7361 (ppt170) cc_final: 0.6924 (ptt-90) REVERT: A 439 MET cc_start: 0.9170 (mmm) cc_final: 0.8705 (mmm) REVERT: B 252 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8793 (tptt) REVERT: B 258 MET cc_start: 0.7918 (mtp) cc_final: 0.7610 (mtp) REVERT: B 331 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 385 ARG cc_start: 0.7742 (ptt90) cc_final: 0.7473 (ptm-80) REVERT: B 386 ASP cc_start: 0.8363 (p0) cc_final: 0.7884 (t70) REVERT: B 389 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: B 439 MET cc_start: 0.9206 (mmm) cc_final: 0.8712 (mmm) REVERT: B 441 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 626 THR cc_start: 0.8756 (p) cc_final: 0.8544 (p) REVERT: B 659 ASN cc_start: 0.8850 (t0) cc_final: 0.8485 (t0) REVERT: B 698 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7303 (mtp) REVERT: C 276 MET cc_start: 0.8274 (tmm) cc_final: 0.8042 (ptm) REVERT: C 385 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: C 533 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7856 (pt0) REVERT: C 546 GLU cc_start: 0.8383 (mp0) cc_final: 0.7821 (mp0) REVERT: C 626 THR cc_start: 0.8846 (p) cc_final: 0.8548 (p) REVERT: C 675 ASP cc_start: 0.7953 (t0) cc_final: 0.7405 (p0) REVERT: C 715 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7669 (tp) REVERT: F 273 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7049 (tt) REVERT: F 276 MET cc_start: -0.1084 (mmm) cc_final: -0.3155 (ttm) REVERT: F 427 MET cc_start: 0.2887 (tpp) cc_final: 0.1969 (tpp) REVERT: F 598 GLN cc_start: 0.7748 (mm110) cc_final: 0.7207 (mm110) REVERT: F 698 MET cc_start: 0.7643 (mmm) cc_final: 0.7083 (mmm) REVERT: D 495 ASN cc_start: 0.9292 (m110) cc_final: 0.8875 (t0) REVERT: D 738 ASP cc_start: 0.8376 (t0) cc_final: 0.8127 (t0) REVERT: D 776 MET cc_start: 0.4086 (mtp) cc_final: 0.3738 (mpp) REVERT: E 368 ILE cc_start: 0.8181 (mm) cc_final: 0.7948 (pt) REVERT: E 373 ASN cc_start: 0.8731 (t0) cc_final: 0.8479 (t0) REVERT: E 439 MET cc_start: 0.8360 (mpp) cc_final: 0.7863 (mpp) REVERT: E 485 MET cc_start: 0.6438 (tmm) cc_final: 0.5999 (tmm) REVERT: E 498 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.6756 (mmmt) REVERT: E 516 MET cc_start: 0.7988 (mtt) cc_final: 0.7778 (mtt) outliers start: 69 outliers final: 56 residues processed: 373 average time/residue: 0.1618 time to fit residues: 98.8652 Evaluate side-chains 382 residues out of total 2689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 745 GLU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 494 THR Chi-restraints excluded: chain F residue 605 VAL Chi-restraints excluded: chain F residue 682 THR Chi-restraints excluded: chain F residue 703 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 498 LYS Chi-restraints excluded: chain E residue 602 TRP Chi-restraints excluded: chain E residue 603 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 672 THR Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 205 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 223 optimal weight: 0.3980 chunk 171 optimal weight: 5.9990 chunk 134 optimal weight: 0.0470 chunk 163 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 58 optimal weight: 0.0870 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 ASN F 309 ASN F 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.119431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095556 restraints weight = 66611.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.098091 restraints weight = 32071.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099725 restraints weight = 19523.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100710 restraints weight = 13972.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101417 restraints weight = 11313.845| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25969 Z= 0.113 Angle : 0.639 12.828 35219 Z= 0.306 Chirality : 0.044 0.327 3998 Planarity : 0.005 0.053 4542 Dihedral : 7.307 158.598 3716 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.45 % Allowed : 21.01 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3201 helix: 0.17 (0.15), residues: 1313 sheet: -0.20 (0.25), residues: 414 loop : -1.31 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 391 TYR 0.009 0.001 TYR A 643 PHE 0.042 0.001 PHE D 376 TRP 0.031 0.001 TRP D 602 HIS 0.004 0.001 HIS D 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (25961) covalent geometry : angle 0.63898 / 0.31 (35219) hydrogen bonds : bond 0.02799 / 1.83 ( 890) hydrogen bonds : angle 4.59224 / 3.18 ( 2499) Misc. bond : bond 0.00080 / 0.05 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5234.85 seconds wall clock time: 91 minutes 10.64 seconds (5470.64 seconds total)