Starting phenix.real_space_refine on Wed Jun 11 02:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9not_49616/06_2025/9not_49616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9not_49616/06_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_49616/06_2025/9not_49616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9not_49616/06_2025/9not_49616.map" model { file = "/net/cci-nas-00/data/ceres_data/9not_49616/06_2025/9not_49616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9not_49616/06_2025/9not_49616.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.31, per 1000 atoms: 0.75 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.57 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: 4.65 Time building geometry restraints manager: 3.85 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.380 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (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 TRP 0.015 0.001 TRP B 564 HIS 0.004 0.001 HIS A 117 PHE 0.032 0.001 PHE B 749 TYR 0.028 0.002 TYR B 394 ARG 0.002 0.000 ARG A 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 16) link_NAG-ASN : angle 3.73428 ( 48) hydrogen bonds : bond 0.12982 ( 607) hydrogen bonds : angle 5.54777 ( 1749) SS BOND : bond 0.00377 ( 20) SS BOND : angle 1.80909 ( 40) covalent geometry : bond 0.00298 (12673) covalent geometry : angle 0.65259 (17268) *********************** 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 : 1.234 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2249 time to fit residues: 45.2234 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 : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.120753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095186 restraints weight = 29166.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093207 restraints weight = 35849.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094327 restraints weight = 32710.685| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12709 Z= 0.148 Angle : 0.635 9.602 17356 Z= 0.302 Chirality : 0.044 0.341 2015 Planarity : 0.004 0.040 2165 Dihedral : 6.399 55.859 2001 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.67 % Allowed : 5.59 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1528 helix: 1.25 (0.19), residues: 748 sheet: -1.47 (0.40), residues: 164 loop : -0.53 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 205 HIS 0.004 0.001 HIS B 469 PHE 0.030 0.001 PHE B 766 TYR 0.032 0.002 TYR B 699 ARG 0.003 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 16) link_NAG-ASN : angle 3.83037 ( 48) hydrogen bonds : bond 0.04109 ( 607) hydrogen bonds : angle 4.55412 ( 1749) SS BOND : bond 0.00213 ( 20) SS BOND : angle 1.17454 ( 40) covalent geometry : bond 0.00339 (12673) covalent geometry : angle 0.60113 (17268) *********************** 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 122 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: B 178 GLU cc_start: 0.7322 (mp0) cc_final: 0.7006 (mp0) REVERT: A 814 MET cc_start: 0.2443 (ppp) cc_final: 0.1789 (ptm) outliers start: 9 outliers final: 4 residues processed: 117 average time/residue: 0.2196 time to fit residues: 39.2868 Evaluate side-chains 110 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 VAL 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 24 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 86 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 189 HIS ** 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 = 0.3924 r_free = 0.3924 target = 0.119301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094737 restraints weight = 29447.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093459 restraints weight = 40741.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094623 restraints weight = 34484.867| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12709 Z= 0.116 Angle : 0.594 9.570 17356 Z= 0.280 Chirality : 0.043 0.349 2015 Planarity : 0.003 0.041 2165 Dihedral : 6.194 55.201 2001 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.97 % Allowed : 9.32 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1528 helix: 1.35 (0.19), residues: 740 sheet: -1.45 (0.38), residues: 169 loop : -0.55 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.003 0.001 HIS B 469 PHE 0.026 0.001 PHE B 745 TYR 0.028 0.001 TYR B 699 ARG 0.002 0.000 ARG A 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 16) link_NAG-ASN : angle 3.59172 ( 48) hydrogen bonds : bond 0.03636 ( 607) hydrogen bonds : angle 4.23601 ( 1749) SS BOND : bond 0.00194 ( 20) SS BOND : angle 0.89490 ( 40) covalent geometry : bond 0.00256 (12673) covalent geometry : angle 0.56270 (17268) *********************** 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: 13 poor density : 116 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 616 MET cc_start: 0.6610 (mtt) cc_final: 0.6198 (tpp) REVERT: A 814 MET cc_start: 0.2654 (ppp) cc_final: 0.1970 (ptm) outliers start: 13 outliers final: 4 residues processed: 123 average time/residue: 0.2080 time to fit residues: 39.5189 Evaluate side-chains 107 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain A residue 422 GLU 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 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.0570 chunk 71 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.5902 ------------------------------------------------------------------------------- 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 73 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 = 0.3916 r_free = 0.3916 target = 0.119019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093849 restraints weight = 29243.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091731 restraints weight = 38999.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092989 restraints weight = 35330.559| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12709 Z= 0.129 Angle : 0.593 9.571 17356 Z= 0.280 Chirality : 0.043 0.347 2015 Planarity : 0.004 0.063 2165 Dihedral : 6.171 55.410 2001 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 10.74 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1528 helix: 1.38 (0.19), residues: 740 sheet: -1.34 (0.39), residues: 159 loop : -0.56 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 461 HIS 0.003 0.001 HIS A 400 PHE 0.041 0.001 PHE B 749 TYR 0.024 0.001 TYR B 699 ARG 0.002 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 16) link_NAG-ASN : angle 3.46381 ( 48) hydrogen bonds : bond 0.03599 ( 607) hydrogen bonds : angle 4.15845 ( 1749) SS BOND : bond 0.00217 ( 20) SS BOND : angle 0.84443 ( 40) covalent geometry : bond 0.00292 (12673) covalent geometry : angle 0.56428 (17268) *********************** 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 135 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7859 (mt) REVERT: A 616 MET cc_start: 0.6972 (mtt) cc_final: 0.6571 (tpp) REVERT: A 814 MET cc_start: 0.2533 (ppp) cc_final: 0.1972 (ptm) outliers start: 25 outliers final: 14 residues processed: 127 average time/residue: 0.1968 time to fit residues: 39.2564 Evaluate side-chains 121 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 178 GLU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.118074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.092703 restraints weight = 29215.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090848 restraints weight = 38106.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091606 restraints weight = 35701.204| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12709 Z= 0.152 Angle : 0.616 11.857 17356 Z= 0.289 Chirality : 0.044 0.346 2015 Planarity : 0.004 0.049 2165 Dihedral : 6.201 55.613 2001 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.16 % Allowed : 12.90 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1528 helix: 1.38 (0.19), residues: 740 sheet: -1.27 (0.40), residues: 154 loop : -0.61 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 461 HIS 0.003 0.001 HIS A 400 PHE 0.035 0.001 PHE B 749 TYR 0.029 0.002 TYR A 769 ARG 0.002 0.000 ARG B 553 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 16) link_NAG-ASN : angle 3.39596 ( 48) hydrogen bonds : bond 0.03639 ( 607) hydrogen bonds : angle 4.12916 ( 1749) SS BOND : bond 0.00230 ( 20) SS BOND : angle 0.82416 ( 40) covalent geometry : bond 0.00354 (12673) covalent geometry : angle 0.58955 (17268) *********************** 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 142 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 800 LEU cc_start: 0.8329 (mm) cc_final: 0.8072 (mp) REVERT: A 616 MET cc_start: 0.6920 (mtt) cc_final: 0.6556 (tpp) REVERT: A 766 MET cc_start: 0.6576 (tpp) cc_final: 0.6365 (mmt) outliers start: 29 outliers final: 16 residues processed: 133 average time/residue: 0.2114 time to fit residues: 44.1982 Evaluate side-chains 128 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 489 THR Chi-restraints excluded: chain B residue 517 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 81 GLU 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 115 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 55 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 73 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.119795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096659 restraints weight = 29632.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095542 restraints weight = 42862.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096548 restraints weight = 39465.304| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12709 Z= 0.111 Angle : 0.583 10.267 17356 Z= 0.274 Chirality : 0.043 0.350 2015 Planarity : 0.003 0.042 2165 Dihedral : 6.055 55.378 2001 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 13.57 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1528 helix: 1.42 (0.19), residues: 746 sheet: -1.35 (0.40), residues: 153 loop : -0.52 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 303 HIS 0.004 0.001 HIS B 341 PHE 0.031 0.001 PHE B 749 TYR 0.025 0.001 TYR A 769 ARG 0.007 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 16) link_NAG-ASN : angle 3.24759 ( 48) hydrogen bonds : bond 0.03410 ( 607) hydrogen bonds : angle 4.04441 ( 1749) SS BOND : bond 0.00195 ( 20) SS BOND : angle 0.80190 ( 40) covalent geometry : bond 0.00244 (12673) covalent geometry : angle 0.55748 (17268) *********************** 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 139 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7840 (mt) REVERT: A 616 MET cc_start: 0.6817 (mtt) cc_final: 0.6519 (tpp) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.2042 time to fit residues: 42.3416 Evaluate side-chains 126 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 178 GLU 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 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 227 VAL 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 33 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 341 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.118162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093877 restraints weight = 29524.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092421 restraints weight = 41667.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093100 restraints weight = 40505.181| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12709 Z= 0.156 Angle : 0.621 9.829 17356 Z= 0.291 Chirality : 0.044 0.344 2015 Planarity : 0.004 0.043 2165 Dihedral : 6.207 55.855 2001 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.72 % Allowed : 14.62 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1528 helix: 1.38 (0.19), residues: 746 sheet: -1.20 (0.41), residues: 146 loop : -0.57 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.009 0.001 HIS B 341 PHE 0.029 0.001 PHE B 749 TYR 0.031 0.002 TYR A 615 ARG 0.002 0.000 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 16) link_NAG-ASN : angle 3.25080 ( 48) hydrogen bonds : bond 0.03641 ( 607) hydrogen bonds : angle 4.07240 ( 1749) SS BOND : bond 0.00235 ( 20) SS BOND : angle 0.83624 ( 40) covalent geometry : bond 0.00363 (12673) covalent geometry : angle 0.59685 (17268) *********************** 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 138 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7846 (mt) REVERT: B 800 LEU cc_start: 0.8418 (mm) cc_final: 0.8109 (mp) REVERT: A 616 MET cc_start: 0.7188 (mtt) cc_final: 0.6719 (tpp) outliers start: 23 outliers final: 18 residues processed: 133 average time/residue: 0.2040 time to fit residues: 42.4924 Evaluate side-chains 128 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 59 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.113728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089244 restraints weight = 29882.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088301 restraints weight = 43663.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089245 restraints weight = 41641.620| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12709 Z= 0.161 Angle : 0.626 9.545 17356 Z= 0.294 Chirality : 0.044 0.344 2015 Planarity : 0.004 0.052 2165 Dihedral : 6.242 55.784 2001 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 15.44 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1528 helix: 1.37 (0.19), residues: 742 sheet: -1.36 (0.42), residues: 148 loop : -0.51 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.004 0.001 HIS B 469 PHE 0.029 0.002 PHE B 749 TYR 0.020 0.002 TYR B 699 ARG 0.004 0.000 ARG B 553 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 16) link_NAG-ASN : angle 3.21728 ( 48) hydrogen bonds : bond 0.03631 ( 607) hydrogen bonds : angle 4.10504 ( 1749) SS BOND : bond 0.00244 ( 20) SS BOND : angle 0.86247 ( 40) covalent geometry : bond 0.00377 (12673) covalent geometry : angle 0.60239 (17268) *********************** 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 137 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7803 (mt) REVERT: B 800 LEU cc_start: 0.8365 (mm) cc_final: 0.8112 (mp) REVERT: B 818 MET cc_start: 0.5468 (mmm) cc_final: 0.4319 (mtp) REVERT: A 616 MET cc_start: 0.7005 (mtt) cc_final: 0.6672 (tpp) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.2223 time to fit residues: 46.3212 Evaluate side-chains 130 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 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 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 107 optimal weight: 0.0770 chunk 152 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 HIS 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.113746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089633 restraints weight = 29814.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088069 restraints weight = 41080.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088811 restraints weight = 41497.126| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12709 Z= 0.128 Angle : 0.620 10.176 17356 Z= 0.290 Chirality : 0.044 0.346 2015 Planarity : 0.004 0.048 2165 Dihedral : 6.130 55.615 2001 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.64 % Allowed : 15.73 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1528 helix: 1.36 (0.19), residues: 750 sheet: -1.23 (0.42), residues: 146 loop : -0.52 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 205 HIS 0.007 0.001 HIS B 341 PHE 0.029 0.001 PHE B 749 TYR 0.032 0.001 TYR A 769 ARG 0.002 0.000 ARG A 383 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 16) link_NAG-ASN : angle 3.09434 ( 48) hydrogen bonds : bond 0.03499 ( 607) hydrogen bonds : angle 4.10171 ( 1749) SS BOND : bond 0.00211 ( 20) SS BOND : angle 0.80484 ( 40) covalent geometry : bond 0.00290 (12673) covalent geometry : angle 0.59834 (17268) *********************** 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 135 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7789 (mt) REVERT: B 818 MET cc_start: 0.5544 (mmm) cc_final: 0.4310 (mtp) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 0.2213 time to fit residues: 45.3624 Evaluate side-chains 125 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.0470 chunk 62 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 107 ASN ** 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 = 0.3865 r_free = 0.3865 target = 0.112281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088486 restraints weight = 29496.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087547 restraints weight = 41603.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088101 restraints weight = 42999.954| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12709 Z= 0.187 Angle : 0.668 10.934 17356 Z= 0.315 Chirality : 0.046 0.339 2015 Planarity : 0.004 0.043 2165 Dihedral : 6.323 56.191 2001 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.49 % Allowed : 15.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1528 helix: 1.24 (0.19), residues: 743 sheet: -1.41 (0.41), residues: 151 loop : -0.51 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.004 0.001 HIS B 469 PHE 0.030 0.002 PHE B 749 TYR 0.029 0.002 TYR A 769 ARG 0.003 0.000 ARG A 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 16) link_NAG-ASN : angle 3.13836 ( 48) hydrogen bonds : bond 0.03840 ( 607) hydrogen bonds : angle 4.21369 ( 1749) SS BOND : bond 0.00272 ( 20) SS BOND : angle 0.85483 ( 40) covalent geometry : bond 0.00443 (12673) covalent geometry : angle 0.64759 (17268) ********************** 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 131 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 385 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7832 (mt) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.2535 time to fit residues: 50.0230 Evaluate side-chains 126 residues out of total 1341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 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 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 134 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.113427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088549 restraints weight = 29540.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086603 restraints weight = 39841.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087815 restraints weight = 38131.398| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2706 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= 0.140 Angle : 0.662 12.340 17356 Z= 0.311 Chirality : 0.045 0.337 2015 Planarity : 0.004 0.042 2165 Dihedral : 6.195 55.572 2001 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.42 % Allowed : 16.26 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1528 helix: 1.25 (0.19), residues: 752 sheet: -1.35 (0.42), residues: 148 loop : -0.52 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 205 HIS 0.004 0.001 HIS B 469 PHE 0.041 0.002 PHE B 766 TYR 0.032 0.001 TYR A 769 ARG 0.006 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 16) link_NAG-ASN : angle 3.02545 ( 48) hydrogen bonds : bond 0.03719 ( 607) hydrogen bonds : angle 4.15127 ( 1749) SS BOND : bond 0.00217 ( 20) SS BOND : angle 0.80059 ( 40) covalent geometry : bond 0.00323 (12673) covalent geometry : angle 0.64291 (17268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3753.12 seconds wall clock time: 67 minutes 25.49 seconds (4045.49 seconds total)