Starting phenix.real_space_refine on Sat Aug 23 13:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.map" model { file = "/net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9not_49616/08_2025/9not_49616.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.042 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 7964 2.51 5 N 2061 2.21 5 O 2238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12359 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6013 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 44, 'TRANS': 730} Chain breaks: 3 Chain: "A" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6122 Classifications: {'peptide': 767} Link IDs: {'PTRANS': 38, 'TRANS': 728} Chain breaks: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 2.51, per 1000 atoms: 0.20 Number of scatterers: 12359 At special positions: 0 Unit cell: (97.114, 91.353, 183.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2238 8.00 N 2061 7.00 C 7964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.02 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.02 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 722 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 720 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 527 " " NAG A 902 " - " ASN A 487 " " NAG A 903 " - " ASN A 84 " " NAG A 904 " - " ASN A 428 " " NAG A 905 " - " ASN A 312 " " NAG A 906 " - " ASN A 248 " " NAG A 907 " - " ASN A 292 " " NAG A 908 " - " ASN A 368 " " NAG B 901 " - " ASN B 475 " " NAG B 902 " - " ASN B 285 " " NAG B 903 " - " ASN B 264 " " NAG B 904 " - " ASN B 411 " " NAG B 905 " - " ASN B 85 " " NAG B 906 " - " ASN B 130 " " NAG B 907 " - " ASN B 380 " " NAG B 908 " - " ASN B 432 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 457.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 53.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.546A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 4.227A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.947A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.503A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.027A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.675A pdb=" N SER B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.521A pdb=" N THR B 305 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.955A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.669A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 385 removed outlier: 4.031A pdb=" N SER B 382 " --> pdb=" O GLN B 379 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.808A pdb=" N SER B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 566 through 593 Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 604 through 622 removed outlier: 3.843A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 664 removed outlier: 5.065A pdb=" N GLN B 637 " --> pdb=" O CYS B 633 " (cutoff:3.500A) Proline residue: B 638 - end of helix Proline residue: B 643 - end of helix removed outlier: 3.658A pdb=" N LEU B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.194A pdb=" N ARG B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 677 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 702 Processing helix chain 'B' and resid 728 through 749 removed outlier: 4.450A pdb=" N THR B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 785 Proline residue: B 780 - end of helix Processing helix chain 'B' and resid 786 through 788 No H-bonds generated for 'chain 'B' and resid 786 through 788' Processing helix chain 'B' and resid 789 through 819 removed outlier: 4.652A pdb=" N LEU B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Proline residue: B 812 - end of helix removed outlier: 3.532A pdb=" N LEU B 816 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 824 removed outlier: 3.878A pdb=" N LEU B 823 " --> pdb=" O GLN B 820 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 824 " --> pdb=" O PRO B 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 820 through 824' Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.961A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.535A pdb=" N LEU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 250 through 266 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 292 removed outlier: 4.385A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.003A pdb=" N HIS A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 5.127A pdb=" N ARG A 317 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.678A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.758A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 563 through 590 Processing helix chain 'A' and resid 593 through 599 Processing helix chain 'A' and resid 600 through 618 Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 626 through 665 Proline residue: A 638 - end of helix removed outlier: 4.458A pdb=" N ALA A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.555A pdb=" N TYR A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 701 Processing helix chain 'A' and resid 723 through 749 removed outlier: 3.881A pdb=" N SER A 727 " --> pdb=" O ASN A 723 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.633A pdb=" N PHE A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 817 removed outlier: 3.783A pdb=" N TYR A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.542A pdb=" N TYR B 97 " --> pdb=" O MET B 31 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 37 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 45 removed outlier: 3.543A pdb=" N ARG B 64 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.440A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.984A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU B 242 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 271 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 324 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 462 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=AA8, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AB2, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.334A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 101 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 34 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA A 137 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.596A pdb=" N GLU A 63 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.448A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.450A pdb=" N ILE A 206 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLU A 238 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 208 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 240 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 210 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TRP A 205 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL A 273 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE A 207 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 209 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 428 through 430 Processing sheet with id=AB7, first strand: chain 'A' and resid 503 through 507 Processing sheet with id=AB8, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AB9, first strand: chain 'A' and resid 555 through 557 removed outlier: 3.649A pdb=" N VAL A 718 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 717 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 707 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 719 " --> pdb=" O THR A 705 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1749 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: 1.95 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3881 1.34 - 1.46: 2786 1.46 - 1.58: 5872 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 12673 Sorted by residual: bond pdb=" CB CYS B 517 " pdb=" SG CYS B 517 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CG LEU B 750 " pdb=" CD2 LEU B 750 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" C PHE B 624 " pdb=" N PRO B 625 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.46e+00 bond pdb=" SD MET B 795 " pdb=" CE MET B 795 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.03e-01 bond pdb=" C VAL B 471 " pdb=" O VAL B 471 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.39e-01 ... (remaining 12668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 16905 1.89 - 3.79: 298 3.79 - 5.68: 51 5.68 - 7.58: 10 7.58 - 9.47: 4 Bond angle restraints: 17268 Sorted by residual: angle pdb=" N VAL A 136 " pdb=" CA VAL A 136 " pdb=" C VAL A 136 " ideal model delta sigma weight residual 113.42 108.07 5.35 1.17e+00 7.31e-01 2.09e+01 angle pdb=" C TRP B 698 " pdb=" N TYR B 699 " pdb=" CA TYR B 699 " ideal model delta sigma weight residual 122.38 116.63 5.75 1.81e+00 3.05e-01 1.01e+01 angle pdb=" C2 NAG A 905 " pdb=" N2 NAG A 905 " pdb=" C7 NAG A 905 " ideal model delta sigma weight residual 124.56 134.03 -9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" C ASN B 824 " pdb=" N THR B 825 " pdb=" CA THR B 825 " ideal model delta sigma weight residual 121.70 116.21 5.49 1.80e+00 3.09e-01 9.31e+00 angle pdb=" CA MET A 697 " pdb=" CB MET A 697 " pdb=" CG MET A 697 " ideal model delta sigma weight residual 114.10 119.82 -5.72 2.00e+00 2.50e-01 8.19e+00 ... (remaining 17263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7006 17.90 - 35.80: 581 35.80 - 53.70: 121 53.70 - 71.60: 27 71.60 - 89.49: 13 Dihedral angle restraints: 7748 sinusoidal: 3246 harmonic: 4502 Sorted by residual: dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 351 " pdb=" CB CYS B 351 " ideal model delta sinusoidal sigma weight residual -86.00 -171.36 85.36 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS B 499 " pdb=" SG CYS B 499 " pdb=" SG CYS B 518 " pdb=" CB CYS B 518 " ideal model delta sinusoidal sigma weight residual -86.00 -8.06 -77.94 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual -86.00 -160.59 74.59 1 1.00e+01 1.00e-02 7.05e+01 ... (remaining 7745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1729 0.061 - 0.121: 267 0.121 - 0.182: 13 0.182 - 0.242: 2 0.242 - 0.302: 4 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C1 NAG A 907 " pdb=" ND2 ASN A 292 " pdb=" C2 NAG A 907 " pdb=" O5 NAG A 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 84 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2012 not shown) Planarity restraints: 2181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 749 " -0.015 2.00e-02 2.50e+03 1.37e-02 3.29e+00 pdb=" CG PHE B 749 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 749 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 749 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 749 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 749 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 749 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 432 " 0.016 2.00e-02 2.50e+03 1.48e-02 2.75e+00 pdb=" CG ASN B 432 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 432 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 432 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG B 908 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 394 " 0.016 2.00e-02 2.50e+03 1.16e-02 2.67e+00 pdb=" CG TYR B 394 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 394 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 394 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 394 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 394 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 394 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 394 " 0.002 2.00e-02 2.50e+03 ... (remaining 2178 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7136 3.02 - 3.49: 13147 3.49 - 3.96: 19634 3.96 - 4.43: 22776 4.43 - 4.90: 36039 Nonbonded interactions: 98732 Sorted by model distance: nonbonded pdb=" O ASN A 487 " pdb=" OD1 ASN A 487 " model vdw 2.550 3.040 nonbonded pdb=" N GLN A 441 " pdb=" OE1 GLN A 441 " model vdw 2.587 3.120 nonbonded pdb=" N GLU A 382 " pdb=" OE1 GLU A 382 " model vdw 2.596 3.120 nonbonded pdb=" N GLN B 418 " pdb=" O GLN B 418 " model vdw 2.626 2.496 nonbonded pdb=" N VAL A 136 " pdb=" N ALA A 137 " model vdw 2.627 2.560 ... (remaining 98727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 10.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.003 0.048 12709 Z= 0.142 Angle : 0.685 9.676 17356 Z= 0.343 Chirality : 0.044 0.302 2015 Planarity : 0.004 0.041 2165 Dihedral : 13.715 89.495 4774 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.22), residues: 1528 helix: 1.16 (0.19), residues: 739 sheet: -1.71 (0.39), residues: 177 loop : -0.55 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.028 0.002 TYR B 394 PHE 0.032 0.001 PHE B 749 TRP 0.015 0.001 TRP B 564 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00298 (12673) covalent geometry : angle 0.65259 (17268) SS BOND : bond 0.00377 ( 20) SS BOND : angle 1.80909 ( 40) hydrogen bonds : bond 0.12982 ( 607) hydrogen bonds : angle 5.54777 ( 1749) link_NAG-ASN : bond 0.00704 ( 16) link_NAG-ASN : angle 3.73428 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 MET cc_start: 0.6162 (mmm) cc_final: 0.5959 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0877 time to fit residues: 17.7002 Evaluate side-chains 108 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 GLN A 291 GLN ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.121563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097053 restraints weight = 29152.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095584 restraints weight = 41614.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096454 restraints weight = 34481.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097691 restraints weight = 24015.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097759 restraints weight = 20516.186| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12709 Z= 0.124 Angle : 0.620 9.560 17356 Z= 0.293 Chirality : 0.043 0.344 2015 Planarity : 0.004 0.040 2165 Dihedral : 6.303 54.888 2001 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1528 helix: 1.30 (0.19), residues: 748 sheet: -1.43 (0.39), residues: 169 loop : -0.51 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 762 TYR 0.033 0.001 TYR B 699 PHE 0.018 0.001 PHE A 641 TRP 0.008 0.001 TRP A 205 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00266 (12673) covalent geometry : angle 0.58602 (17268) SS BOND : bond 0.00211 ( 20) SS BOND : angle 1.12067 ( 40) hydrogen bonds : bond 0.03873 ( 607) hydrogen bonds : angle 4.44906 ( 1749) link_NAG-ASN : bond 0.00736 ( 16) link_NAG-ASN : angle 3.78026 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7111 (mp0) cc_final: 0.6765 (mp0) REVERT: B 768 MET cc_start: 0.6858 (mmp) cc_final: 0.6505 (tpp) REVERT: A 814 MET cc_start: 0.2597 (ppp) cc_final: 0.1972 (ptm) outliers start: 8 outliers final: 3 residues processed: 119 average time/residue: 0.0759 time to fit residues: 14.0463 Evaluate side-chains 109 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 711 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 72 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093826 restraints weight = 29524.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092248 restraints weight = 36449.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092973 restraints weight = 35803.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094246 restraints weight = 24435.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094226 restraints weight = 20054.797| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12709 Z= 0.135 Angle : 0.597 9.564 17356 Z= 0.282 Chirality : 0.043 0.347 2015 Planarity : 0.003 0.041 2165 Dihedral : 6.231 55.410 2001 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.04 % Allowed : 9.55 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.22), residues: 1528 helix: 1.36 (0.19), residues: 740 sheet: -1.40 (0.38), residues: 169 loop : -0.53 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.029 0.002 TYR A 769 PHE 0.013 0.001 PHE B 730 TRP 0.010 0.001 TRP B 461 HIS 0.003 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00309 (12673) covalent geometry : angle 0.56632 (17268) SS BOND : bond 0.00205 ( 20) SS BOND : angle 0.92446 ( 40) hydrogen bonds : bond 0.03711 ( 607) hydrogen bonds : angle 4.22505 ( 1749) link_NAG-ASN : bond 0.00640 ( 16) link_NAG-ASN : angle 3.59547 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7201 (mp0) cc_final: 0.6940 (mp0) REVERT: A 814 MET cc_start: 0.2649 (ppp) cc_final: 0.2038 (ptm) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.0828 time to fit residues: 15.7940 Evaluate side-chains 115 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 66 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS ** A 555 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.119643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094561 restraints weight = 29278.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.093205 restraints weight = 37540.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094223 restraints weight = 36115.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094450 restraints weight = 23336.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094802 restraints weight = 21596.485| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12709 Z= 0.109 Angle : 0.571 9.571 17356 Z= 0.270 Chirality : 0.042 0.350 2015 Planarity : 0.004 0.064 2165 Dihedral : 6.089 55.271 2001 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.57 % Allowed : 11.11 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.22), residues: 1528 helix: 1.38 (0.19), residues: 740 sheet: -1.37 (0.38), residues: 169 loop : -0.48 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 762 TYR 0.029 0.001 TYR A 615 PHE 0.015 0.001 PHE B 749 TRP 0.008 0.001 TRP A 304 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00238 (12673) covalent geometry : angle 0.54204 (17268) SS BOND : bond 0.00181 ( 20) SS BOND : angle 0.78353 ( 40) hydrogen bonds : bond 0.03509 ( 607) hydrogen bonds : angle 4.08358 ( 1749) link_NAG-ASN : bond 0.00668 ( 16) link_NAG-ASN : angle 3.42396 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7259 (mp0) cc_final: 0.7020 (mp0) REVERT: B 385 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7844 (mt) REVERT: A 814 MET cc_start: 0.2512 (ppp) cc_final: 0.1966 (ptm) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.0803 time to fit residues: 16.2209 Evaluate side-chains 123 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 101 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 66 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.119412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094945 restraints weight = 29398.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093853 restraints weight = 40176.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094570 restraints weight = 37122.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095866 restraints weight = 24930.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095878 restraints weight = 19706.437| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12709 Z= 0.127 Angle : 0.595 9.558 17356 Z= 0.281 Chirality : 0.043 0.348 2015 Planarity : 0.004 0.048 2165 Dihedral : 6.095 55.449 2001 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 13.12 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1528 helix: 1.37 (0.19), residues: 744 sheet: -1.30 (0.38), residues: 169 loop : -0.45 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 762 TYR 0.028 0.001 TYR A 769 PHE 0.017 0.001 PHE A 745 TRP 0.008 0.001 TRP A 205 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00287 (12673) covalent geometry : angle 0.56928 (17268) SS BOND : bond 0.00189 ( 20) SS BOND : angle 0.75005 ( 40) hydrogen bonds : bond 0.03527 ( 607) hydrogen bonds : angle 4.10952 ( 1749) link_NAG-ASN : bond 0.00641 ( 16) link_NAG-ASN : angle 3.33072 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 800 LEU cc_start: 0.8294 (mm) cc_final: 0.8036 (mp) outliers start: 25 outliers final: 15 residues processed: 137 average time/residue: 0.0770 time to fit residues: 16.5089 Evaluate side-chains 129 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094988 restraints weight = 29239.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094291 restraints weight = 39710.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094924 restraints weight = 39169.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095224 restraints weight = 23512.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095602 restraints weight = 21212.826| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12709 Z= 0.143 Angle : 0.608 11.688 17356 Z= 0.287 Chirality : 0.043 0.346 2015 Planarity : 0.004 0.043 2165 Dihedral : 6.144 55.573 2001 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 13.65 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1528 helix: 1.37 (0.19), residues: 744 sheet: -1.26 (0.39), residues: 159 loop : -0.52 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 762 TYR 0.024 0.001 TYR B 699 PHE 0.020 0.001 PHE B 742 TRP 0.008 0.001 TRP B 303 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00330 (12673) covalent geometry : angle 0.58334 (17268) SS BOND : bond 0.00229 ( 20) SS BOND : angle 0.81590 ( 40) hydrogen bonds : bond 0.03578 ( 607) hydrogen bonds : angle 4.12666 ( 1749) link_NAG-ASN : bond 0.00617 ( 16) link_NAG-ASN : angle 3.29834 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7358 (mp0) cc_final: 0.7040 (mp0) REVERT: B 385 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7880 (mt) REVERT: A 607 MET cc_start: 0.6651 (mmm) cc_final: 0.6099 (mmm) outliers start: 29 outliers final: 18 residues processed: 138 average time/residue: 0.0814 time to fit residues: 17.8196 Evaluate side-chains 129 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 127 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094307 restraints weight = 29591.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092624 restraints weight = 43570.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093344 restraints weight = 42517.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094868 restraints weight = 27916.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094856 restraints weight = 20648.993| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12709 Z= 0.168 Angle : 0.628 10.632 17356 Z= 0.298 Chirality : 0.044 0.345 2015 Planarity : 0.004 0.043 2165 Dihedral : 6.250 55.793 2001 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.86 % Allowed : 14.17 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1528 helix: 1.31 (0.19), residues: 744 sheet: -1.26 (0.42), residues: 141 loop : -0.55 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 762 TYR 0.028 0.002 TYR A 769 PHE 0.019 0.001 PHE B 742 TRP 0.010 0.001 TRP A 543 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00393 (12673) covalent geometry : angle 0.60373 (17268) SS BOND : bond 0.00249 ( 20) SS BOND : angle 0.85865 ( 40) hydrogen bonds : bond 0.03756 ( 607) hydrogen bonds : angle 4.15014 ( 1749) link_NAG-ASN : bond 0.00609 ( 16) link_NAG-ASN : angle 3.27812 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7862 (mt) REVERT: B 800 LEU cc_start: 0.8365 (mm) cc_final: 0.8050 (mp) REVERT: A 607 MET cc_start: 0.6720 (mmm) cc_final: 0.6190 (mmm) outliers start: 25 outliers final: 19 residues processed: 135 average time/residue: 0.0766 time to fit residues: 16.4974 Evaluate side-chains 132 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.114152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089786 restraints weight = 29902.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088868 restraints weight = 42390.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089728 restraints weight = 42475.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090035 restraints weight = 25765.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090394 restraints weight = 23109.312| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12709 Z= 0.152 Angle : 0.627 10.341 17356 Z= 0.297 Chirality : 0.044 0.345 2015 Planarity : 0.004 0.055 2165 Dihedral : 6.216 55.639 2001 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.57 % Allowed : 15.21 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.22), residues: 1528 helix: 1.35 (0.19), residues: 740 sheet: -1.26 (0.42), residues: 146 loop : -0.57 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 762 TYR 0.035 0.002 TYR A 615 PHE 0.021 0.001 PHE B 742 TRP 0.011 0.001 TRP A 588 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00354 (12673) covalent geometry : angle 0.60349 (17268) SS BOND : bond 0.00233 ( 20) SS BOND : angle 0.86779 ( 40) hydrogen bonds : bond 0.03689 ( 607) hydrogen bonds : angle 4.11837 ( 1749) link_NAG-ASN : bond 0.00616 ( 16) link_NAG-ASN : angle 3.21604 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: B 162 MET cc_start: 0.8561 (tpp) cc_final: 0.8268 (ttm) REVERT: B 178 GLU cc_start: 0.7421 (mp0) cc_final: 0.7072 (mp0) REVERT: B 385 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7820 (mt) REVERT: B 800 LEU cc_start: 0.8349 (mm) cc_final: 0.8087 (mp) REVERT: B 818 MET cc_start: 0.5368 (mmm) cc_final: 0.4250 (mtp) REVERT: A 607 MET cc_start: 0.6636 (mmm) cc_final: 0.6167 (mmm) outliers start: 21 outliers final: 19 residues processed: 134 average time/residue: 0.0783 time to fit residues: 16.3915 Evaluate side-chains 131 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 HIS ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.113983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088872 restraints weight = 30001.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087399 restraints weight = 40133.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088046 restraints weight = 41315.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089540 restraints weight = 26782.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089562 restraints weight = 19368.008| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12709 Z= 0.147 Angle : 0.634 10.359 17356 Z= 0.300 Chirality : 0.044 0.346 2015 Planarity : 0.004 0.048 2165 Dihedral : 6.206 55.636 2001 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.86 % Allowed : 15.59 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.22), residues: 1528 helix: 1.31 (0.19), residues: 740 sheet: -1.30 (0.41), residues: 149 loop : -0.54 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 589 TYR 0.047 0.002 TYR A 615 PHE 0.027 0.001 PHE B 742 TRP 0.011 0.001 TRP A 588 HIS 0.006 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00339 (12673) covalent geometry : angle 0.61181 (17268) SS BOND : bond 0.00225 ( 20) SS BOND : angle 0.85064 ( 40) hydrogen bonds : bond 0.03794 ( 607) hydrogen bonds : angle 4.14684 ( 1749) link_NAG-ASN : bond 0.00616 ( 16) link_NAG-ASN : angle 3.16767 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 162 MET cc_start: 0.8540 (tpp) cc_final: 0.8276 (ttm) REVERT: B 385 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7783 (mt) REVERT: B 800 LEU cc_start: 0.8387 (mm) cc_final: 0.8147 (mp) REVERT: B 818 MET cc_start: 0.5586 (mmm) cc_final: 0.4441 (mtp) REVERT: A 607 MET cc_start: 0.6862 (mmm) cc_final: 0.6354 (mmm) REVERT: A 661 MET cc_start: 0.5691 (mtt) cc_final: 0.5334 (tmm) outliers start: 25 outliers final: 20 residues processed: 132 average time/residue: 0.0823 time to fit residues: 17.1733 Evaluate side-chains 131 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 110 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089861 restraints weight = 29742.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.088465 restraints weight = 44446.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089125 restraints weight = 43043.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090650 restraints weight = 27984.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.090575 restraints weight = 20651.151| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12709 Z= 0.157 Angle : 0.667 13.082 17356 Z= 0.317 Chirality : 0.045 0.344 2015 Planarity : 0.004 0.043 2165 Dihedral : 6.212 55.712 2001 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 15.81 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1528 helix: 1.24 (0.19), residues: 742 sheet: -1.31 (0.41), residues: 149 loop : -0.55 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.020 0.002 TYR A 621 PHE 0.030 0.001 PHE B 742 TRP 0.012 0.001 TRP A 588 HIS 0.004 0.001 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00363 (12673) covalent geometry : angle 0.64638 (17268) SS BOND : bond 0.00233 ( 20) SS BOND : angle 0.86011 ( 40) hydrogen bonds : bond 0.03828 ( 607) hydrogen bonds : angle 4.22717 ( 1749) link_NAG-ASN : bond 0.00609 ( 16) link_NAG-ASN : angle 3.14188 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: B 162 MET cc_start: 0.8583 (tpp) cc_final: 0.8261 (ttm) REVERT: B 385 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 800 LEU cc_start: 0.8296 (mm) cc_final: 0.8049 (mp) REVERT: B 818 MET cc_start: 0.5546 (mmm) cc_final: 0.4270 (mtp) REVERT: A 603 MET cc_start: 0.6492 (mmt) cc_final: 0.6209 (mmt) REVERT: A 607 MET cc_start: 0.6694 (mmm) cc_final: 0.6249 (mmm) REVERT: A 661 MET cc_start: 0.5379 (mtt) cc_final: 0.5174 (tmm) outliers start: 23 outliers final: 20 residues processed: 133 average time/residue: 0.0719 time to fit residues: 15.2269 Evaluate side-chains 131 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 341 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 590 HIS Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 720 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.113726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089607 restraints weight = 29717.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088543 restraints weight = 37302.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089420 restraints weight = 37659.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089701 restraints weight = 23379.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089961 restraints weight = 21558.045| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12709 Z= 0.155 Angle : 0.675 12.676 17356 Z= 0.321 Chirality : 0.045 0.340 2015 Planarity : 0.004 0.046 2165 Dihedral : 6.219 55.675 2001 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 16.03 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1528 helix: 1.26 (0.19), residues: 739 sheet: -1.37 (0.41), residues: 151 loop : -0.48 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 589 TYR 0.032 0.001 TYR A 769 PHE 0.030 0.002 PHE B 742 TRP 0.013 0.001 TRP A 588 HIS 0.006 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00357 (12673) covalent geometry : angle 0.65549 (17268) SS BOND : bond 0.00226 ( 20) SS BOND : angle 0.85772 ( 40) hydrogen bonds : bond 0.03851 ( 607) hydrogen bonds : angle 4.25905 ( 1749) link_NAG-ASN : bond 0.00615 ( 16) link_NAG-ASN : angle 3.08971 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.28 seconds wall clock time: 28 minutes 13.17 seconds (1693.17 seconds total)