Starting phenix.real_space_refine on Sun May 3 18:49:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.map" model { file = "/net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wyt_66376/05_2026/9wyt_66376.cif" } resolution = 3.06 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= -0.000 sd= 0.028 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 88 5.16 5 C 9217 2.51 5 N 2446 2.21 5 O 2774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14525 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1707 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 217, 1704 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1746 Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 194} Chain breaks: 1 Chain: "J" Number of atoms: 10832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1326, 10832 Classifications: {'peptide': 1326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 44, 'TRANS': 1277} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.50, per 1000 atoms: 0.24 Number of scatterers: 14525 At special positions: 0 Unit cell: (109.62, 103.53, 134.85, 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 88 16.00 O 2774 8.00 N 2446 7.00 C 9217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 431 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 546 " distance=2.02 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 62 " distance=2.03 Simple disulfide: pdb=" SG CYS J 87 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 115 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 200 " distance=2.02 Simple disulfide: pdb=" SG CYS J 190 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 222 " - pdb=" SG CYS J 235 " distance=2.03 Simple disulfide: pdb=" SG CYS J 253 " - pdb=" SG CYS J 350 " distance=2.03 Simple disulfide: pdb=" SG CYS J 326 " - pdb=" SG CYS J 342 " distance=2.03 Simple disulfide: pdb=" SG CYS J 372 " - pdb=" SG CYS J 383 " distance=2.04 Simple disulfide: pdb=" SG CYS J 400 " - pdb=" SG CYS J 495 " distance=2.03 Simple disulfide: pdb=" SG CYS J 472 " - pdb=" SG CYS J 487 " distance=2.05 Simple disulfide: pdb=" SG CYS J 512 " - pdb=" SG CYS J 523 " distance=2.03 Simple disulfide: pdb=" SG CYS J 542 " - pdb=" SG CYS J 640 " distance=2.03 Simple disulfide: pdb=" SG CYS J 614 " - pdb=" SG CYS J 631 " distance=2.02 Simple disulfide: pdb=" SG CYS J 661 " - pdb=" SG CYS J 674 " distance=2.03 Simple disulfide: pdb=" SG CYS J 696 " - pdb=" SG CYS J 793 " distance=1.99 Simple disulfide: pdb=" SG CYS J 771 " - pdb=" SG CYS J 785 " distance=2.03 Simple disulfide: pdb=" SG CYS J 837 " - pdb=" SG CYS J 934 " distance=2.03 Simple disulfide: pdb=" SG CYS J 911 " - pdb=" SG CYS J 926 " distance=2.03 Simple disulfide: pdb=" SG CYS J 956 " - pdb=" SG CYS J 967 " distance=2.04 Simple disulfide: pdb=" SG CYS J 989 " - pdb=" SG CYS J1093 " distance=2.02 Simple disulfide: pdb=" SG CYS J1065 " - pdb=" SG CYS J1085 " distance=2.03 Simple disulfide: pdb=" SG CYS J1139 " - pdb=" SG CYS J1229 " distance=2.03 Simple disulfide: pdb=" SG CYS J1206 " - pdb=" SG CYS J1220 " distance=2.04 Simple disulfide: pdb=" SG CYS J1244 " - pdb=" SG CYS J1258 " distance=2.03 Simple disulfide: pdb=" SG CYS J1277 " - pdb=" SG CYS J1374 " distance=2.03 Simple disulfide: pdb=" SG CYS J1351 " - pdb=" SG CYS J1366 " 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 ALPHA1-2 " MAN A 604 " - " MAN A 607 " " MAN A 607 " - " MAN A 608 " " MAN B 604 " - " MAN B 606 " ALPHA1-3 " BMA A 603 " - " MAN A 604 " " MAN A 605 " - " MAN A 606 " " BMA B 603 " - " MAN B 604 " " MAN B 605 " - " MAN B 608 " ALPHA1-6 " BMA A 603 " - " MAN A 605 " " BMA B 603 " - " MAN B 605 " " MAN B 605 " - " MAN B 607 " BETA1-4 " NAG A 601 " - " NAG A 602 " " NAG A 602 " - " BMA A 603 " " NAG B 601 " - " NAG B 602 " " NAG B 602 " - " BMA B 603 " " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 407 " " NAG B 601 " - " ASN B 407 " " NAG C 1 " - " ASN J 777 " " NAG J1501 " - " ASN J 91 " " NAG J1502 " - " ASN J 581 " " NAG J1503 " - " ASN J 274 " " NAG J1504 " - " ASN J 427 " " NAG J1505 " - " ASN J 925 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 654.0 milliseconds 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3314 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 35 sheets defined 17.4% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.737A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 426 removed outlier: 3.669A pdb=" N GLY B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.969A pdb=" N SER B 469 " --> pdb=" O PRO B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.797A pdb=" N GLY B 541 " --> pdb=" O LYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'J' and resid 28 through 37 removed outlier: 4.552A pdb=" N SER J 32 " --> pdb=" O ASP J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 68 No H-bonds generated for 'chain 'J' and resid 66 through 68' Processing helix chain 'J' and resid 75 through 77 No H-bonds generated for 'chain 'J' and resid 75 through 77' Processing helix chain 'J' and resid 107 through 112 removed outlier: 4.068A pdb=" N LEU J 111 " --> pdb=" O ASN J 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP J 112 " --> pdb=" O ARG J 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 107 through 112' Processing helix chain 'J' and resid 122 through 126 removed outlier: 3.874A pdb=" N GLU J 125 " --> pdb=" O GLY J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 255 Processing helix chain 'J' and resid 265 through 277 Processing helix chain 'J' and resid 361 through 366 removed outlier: 3.620A pdb=" N TRP J 365 " --> pdb=" O THR J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 403 Processing helix chain 'J' and resid 413 through 426 removed outlier: 3.674A pdb=" N GLN J 424 " --> pdb=" O HIS J 420 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU J 426 " --> pdb=" O LEU J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 443 removed outlier: 3.583A pdb=" N VAL J 443 " --> pdb=" O ILE J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 532 through 537 Processing helix chain 'J' and resid 551 through 565 removed outlier: 3.857A pdb=" N VAL J 565 " --> pdb=" O MET J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 570 removed outlier: 4.187A pdb=" N ARG J 570 " --> pdb=" O LYS J 567 " (cutoff:3.500A) Processing helix chain 'J' and resid 688 through 695 removed outlier: 3.534A pdb=" N THR J 694 " --> pdb=" O SER J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 708 through 723 removed outlier: 3.559A pdb=" N GLU J 712 " --> pdb=" O HIS J 708 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE J 723 " --> pdb=" O LEU J 719 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 743 removed outlier: 3.910A pdb=" N SER J 742 " --> pdb=" O ASN J 739 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY J 743 " --> pdb=" O PRO J 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 739 through 743' Processing helix chain 'J' and resid 829 through 840 removed outlier: 3.652A pdb=" N VAL J 838 " --> pdb=" O GLU J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 849 through 862 removed outlier: 4.195A pdb=" N LYS J 862 " --> pdb=" O ASN J 858 " (cutoff:3.500A) Processing helix chain 'J' and resid 981 through 992 Processing helix chain 'J' and resid 1001 through 1011 Processing helix chain 'J' and resid 1025 through 1030 Processing helix chain 'J' and resid 1131 through 1142 removed outlier: 3.900A pdb=" N ASN J1142 " --> pdb=" O ALA J1138 " (cutoff:3.500A) Processing helix chain 'J' and resid 1151 through 1166 Processing helix chain 'J' and resid 1269 through 1280 Processing helix chain 'J' and resid 1289 through 1301 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.660A pdb=" N THR A 388 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 430 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS A 431 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 444 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 442 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 404 removed outlier: 3.822A pdb=" N VAL A 401 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 413 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 482 removed outlier: 3.520A pdb=" N VAL A 479 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE A 525 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 492 removed outlier: 3.891A pdb=" N GLU A 488 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 351 through 355 removed outlier: 5.359A pdb=" N ARG B 371 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 416 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU B 373 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER B 414 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL B 375 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 412 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.710A pdb=" N CYS B 431 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 444 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 442 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 457 through 459 removed outlier: 5.848A pdb=" N PHE B 525 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 457 through 459 removed outlier: 5.848A pdb=" N PHE B 525 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 544 through 549 Processing sheet with id=AB3, first strand: chain 'J' and resid 100 through 102 removed outlier: 3.632A pdb=" N SER J 86 " --> pdb=" O ASN J 81 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU J 79 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 147 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'J' and resid 114 through 116 removed outlier: 3.581A pdb=" N ALA J 119 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 127 through 131 Processing sheet with id=AB7, first strand: chain 'J' and resid 180 through 181 Processing sheet with id=AB8, first strand: chain 'J' and resid 199 through 201 Processing sheet with id=AB9, first strand: chain 'J' and resid 227 through 229 removed outlier: 3.724A pdb=" N VAL J 234 " --> pdb=" O ASN J 229 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE J 348 " --> pdb=" O ASN J 239 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER J 241 " --> pdb=" O LEU J 346 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU J 346 " --> pdb=" O SER J 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 285 through 287 Processing sheet with id=AC2, first strand: chain 'J' and resid 377 through 378 removed outlier: 5.728A pdb=" N GLU J 389 " --> pdb=" O ASN J 491 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASN J 491 " --> pdb=" O GLU J 389 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 445 through 446 removed outlier: 3.597A pdb=" N ILE J 433 " --> pdb=" O VAL J 473 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL J 473 " --> pdb=" O ILE J 433 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU J 435 " --> pdb=" O LEU J 471 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU J 471 " --> pdb=" O LEU J 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 517 through 519 removed outlier: 3.623A pdb=" N TYR J 522 " --> pdb=" O HIS J 519 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 525 " --> pdb=" O CYS J 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS J 641 " --> pdb=" O ALA J 545 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA J 545 " --> pdb=" O LYS J 641 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 587 through 588 removed outlier: 3.691A pdb=" N ILE J 575 " --> pdb=" O VAL J 615 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL J 615 " --> pdb=" O ILE J 575 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 673 through 675 Processing sheet with id=AC7, first strand: chain 'J' and resid 735 through 736 Processing sheet with id=AC8, first strand: chain 'J' and resid 771 through 772 Processing sheet with id=AC9, first strand: chain 'J' and resid 813 through 816 removed outlier: 6.222A pdb=" N ASN J 826 " --> pdb=" O LEU J 930 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU J 930 " --> pdb=" O ASN J 826 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 884 through 885 removed outlier: 3.713A pdb=" N ARG J 884 " --> pdb=" O HIS J 875 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE J 872 " --> pdb=" O ILE J 914 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE J 914 " --> pdb=" O ILE J 872 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU J 874 " --> pdb=" O GLY J 912 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 961 through 963 Processing sheet with id=AD3, first strand: chain 'J' and resid 961 through 963 removed outlier: 6.124A pdb=" N ALA J1022 " --> pdb=" O VAL J1092 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N GLN J1094 " --> pdb=" O ALA J1022 " (cutoff:3.500A) removed outlier: 15.346A pdb=" N GLN J1024 " --> pdb=" O GLN J1094 " (cutoff:3.500A) removed outlier: 21.043A pdb=" N GLY J1096 " --> pdb=" O GLN J1024 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR J1066 " --> pdb=" O ILE J1021 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE J1023 " --> pdb=" O LEU J1064 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU J1064 " --> pdb=" O PHE J1023 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS J1079 " --> pdb=" O SER J1069 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 1117 through 1118 Processing sheet with id=AD5, first strand: chain 'J' and resid 1182 through 1184 removed outlier: 4.863A pdb=" N VAL J1207 " --> pdb=" O ILE J1171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 1252 through 1254 Processing sheet with id=AD7, first strand: chain 'J' and resid 1323 through 1324 removed outlier: 5.200A pdb=" N TRP J1311 " --> pdb=" O LEU J1354 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU J1354 " --> pdb=" O TRP J1311 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN J1313 " --> pdb=" O ILE J1352 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE J1352 " --> pdb=" O ASN J1313 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1323 through 1324 removed outlier: 7.306A pdb=" N MET J1309 " --> pdb=" O GLY J1371 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1058 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4415 1.34 - 1.46: 3968 1.46 - 1.58: 6449 1.58 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 14943 Sorted by residual: bond pdb=" CA ALA J 616 " pdb=" C ALA J 616 " ideal model delta sigma weight residual 1.522 1.467 0.055 1.27e-02 6.20e+03 1.85e+01 bond pdb=" CA CYS J 696 " pdb=" CB CYS J 696 " ideal model delta sigma weight residual 1.537 1.498 0.039 1.38e-02 5.25e+03 8.15e+00 bond pdb=" CA CYS J 696 " pdb=" C CYS J 696 " ideal model delta sigma weight residual 1.520 1.483 0.037 1.39e-02 5.18e+03 7.24e+00 bond pdb=" C GLN J 697 " pdb=" N ASP J 698 " ideal model delta sigma weight residual 1.335 1.301 0.034 1.35e-02 5.49e+03 6.24e+00 bond pdb=" N LYS J 632 " pdb=" CA LYS J 632 " ideal model delta sigma weight residual 1.456 1.426 0.030 1.22e-02 6.72e+03 6.17e+00 ... (remaining 14938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 19845 2.76 - 5.52: 398 5.52 - 8.29: 46 8.29 - 11.05: 12 11.05 - 13.81: 1 Bond angle restraints: 20302 Sorted by residual: angle pdb=" N VAL J 615 " pdb=" CA VAL J 615 " pdb=" C VAL J 615 " ideal model delta sigma weight residual 109.80 118.11 -8.31 1.33e+00 5.65e-01 3.90e+01 angle pdb=" C ASN J 439 " pdb=" N ILE J 440 " pdb=" CA ILE J 440 " ideal model delta sigma weight residual 121.97 131.48 -9.51 1.80e+00 3.09e-01 2.79e+01 angle pdb=" CA CYS J 631 " pdb=" CB CYS J 631 " pdb=" SG CYS J 631 " ideal model delta sigma weight residual 114.40 103.68 10.72 2.30e+00 1.89e-01 2.17e+01 angle pdb=" N CYS J 696 " pdb=" CA CYS J 696 " pdb=" C CYS J 696 " ideal model delta sigma weight residual 114.31 108.37 5.94 1.29e+00 6.01e-01 2.12e+01 angle pdb=" N ALA J 616 " pdb=" CA ALA J 616 " pdb=" C ALA J 616 " ideal model delta sigma weight residual 109.14 102.34 6.80 1.49e+00 4.50e-01 2.09e+01 ... (remaining 20297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 8120 23.81 - 47.61: 854 47.61 - 71.42: 147 71.42 - 95.23: 42 95.23 - 119.04: 3 Dihedral angle restraints: 9166 sinusoidal: 4024 harmonic: 5142 Sorted by residual: dihedral pdb=" CB CYS A 347 " pdb=" SG CYS A 347 " pdb=" SG CYS B 347 " pdb=" CB CYS B 347 " ideal model delta sinusoidal sigma weight residual 93.00 176.24 -83.24 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS J 372 " pdb=" SG CYS J 372 " pdb=" SG CYS J 383 " pdb=" CB CYS J 383 " ideal model delta sinusoidal sigma weight residual -86.00 -165.10 79.10 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS J 661 " pdb=" SG CYS J 661 " pdb=" SG CYS J 674 " pdb=" CB CYS J 674 " ideal model delta sinusoidal sigma weight residual -86.00 -160.99 74.99 1 1.00e+01 1.00e-02 7.11e+01 ... (remaining 9163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1653 0.058 - 0.117: 449 0.117 - 0.175: 72 0.175 - 0.234: 13 0.234 - 0.292: 3 Chirality restraints: 2190 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN J 777 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE J 733 " pdb=" CA ILE J 733 " pdb=" CG1 ILE J 733 " pdb=" CG2 ILE J 733 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.72e+00 ... (remaining 2187 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY J 612 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLY J 612 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY J 612 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY J 613 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 107 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" CG ASN J 107 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN J 107 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN J 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 833 " 0.026 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR J 833 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR J 833 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR J 833 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 833 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR J 833 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR J 833 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 833 " -0.003 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3093 2.77 - 3.30: 12289 3.30 - 3.84: 25418 3.84 - 4.37: 29394 4.37 - 4.90: 51984 Nonbonded interactions: 122178 Sorted by model distance: nonbonded pdb=" O SER A 381 " pdb=" OG SER A 381 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASN J1070 " pdb=" OH TYR J1153 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 532 " pdb=" OE2 GLU B 512 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 476 " pdb=" OH TYR A 528 " model vdw 2.281 3.040 nonbonded pdb=" O THR B 432 " pdb=" OG1 THR B 432 " model vdw 2.300 3.040 ... (remaining 122173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 346 through 515 or resid 523 through 557 or resid 559 thro \ ugh 608)) selection = (chain 'B' and (resid 346 through 379 or (resid 380 and (name N or name CA or na \ me C or name O or name CB )) or resid 381 through 515 or resid 523 through 557 o \ r resid 559 through 565 or resid 601 through 608)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.070 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.750 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 14999 Z= 0.356 Angle : 0.935 13.809 20438 Z= 0.496 Chirality : 0.055 0.292 2190 Planarity : 0.007 0.058 2564 Dihedral : 18.873 119.037 5756 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.90 % Favored : 92.76 % Rotamer: Outliers : 6.33 % Allowed : 28.26 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.18), residues: 1741 helix: -3.04 (0.19), residues: 256 sheet: -1.23 (0.26), residues: 405 loop : -1.58 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 493 TYR 0.053 0.003 TYR J 833 PHE 0.047 0.003 PHE J 781 TRP 0.036 0.003 TRP A 491 HIS 0.008 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00801 (14943) covalent geometry : angle 0.91954 (20302) SS BOND : bond 0.00981 ( 32) SS BOND : angle 1.90860 ( 64) hydrogen bonds : bond 0.24223 ( 377) hydrogen bonds : angle 9.37037 ( 1058) link_ALPHA1-2 : bond 0.01082 ( 3) link_ALPHA1-2 : angle 1.88273 ( 9) link_ALPHA1-3 : bond 0.01017 ( 4) link_ALPHA1-3 : angle 2.23696 ( 12) link_ALPHA1-6 : bond 0.00454 ( 3) link_ALPHA1-6 : angle 1.79081 ( 9) link_BETA1-4 : bond 0.00500 ( 5) link_BETA1-4 : angle 3.72352 ( 15) link_BETA1-6 : bond 0.00244 ( 1) link_BETA1-6 : angle 1.45837 ( 3) link_NAG-ASN : bond 0.00561 ( 8) link_NAG-ASN : angle 2.40241 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 153 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 SER cc_start: 0.5911 (OUTLIER) cc_final: 0.5020 (t) REVERT: A 410 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6732 (t80) REVERT: A 488 GLU cc_start: 0.7702 (pp20) cc_final: 0.7208 (pp20) REVERT: B 391 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8042 (tttp) REVERT: B 404 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: B 534 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: J 31 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8719 (Cg_endo) REVERT: J 77 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7800 (mtp-110) REVERT: J 107 ASN cc_start: 0.7540 (p0) cc_final: 0.7142 (p0) REVERT: J 134 LYS cc_start: 0.7882 (tppt) cc_final: 0.7286 (ttmt) REVERT: J 141 LYS cc_start: 0.8424 (mppt) cc_final: 0.8097 (mmmt) REVERT: J 333 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8909 (pp) REVERT: J 363 ASP cc_start: 0.8616 (m-30) cc_final: 0.8086 (t0) REVERT: J 401 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: J 485 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7809 (mmtm) REVERT: J 735 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8816 (t80) REVERT: J 886 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8130 (tptp) REVERT: J 906 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7050 (mppt) REVERT: J 958 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6951 (mttt) REVERT: J 1031 TRP cc_start: 0.6391 (OUTLIER) cc_final: 0.5952 (m100) REVERT: J 1101 ARG cc_start: 0.4862 (OUTLIER) cc_final: 0.2982 (pmt-80) REVERT: J 1120 ASN cc_start: 0.7901 (t0) cc_final: 0.7693 (t0) REVERT: J 1234 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7064 (mttt) outliers start: 99 outliers final: 65 residues processed: 234 average time/residue: 0.1208 time to fit residues: 41.7755 Evaluate side-chains 218 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 361 THR Chi-restraints excluded: chain J residue 370 THR Chi-restraints excluded: chain J residue 371 ARG Chi-restraints excluded: chain J residue 401 GLN Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 485 LYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 583 THR Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 606 HIS Chi-restraints excluded: chain J residue 667 SER Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 696 CYS Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 733 ILE Chi-restraints excluded: chain J residue 735 PHE Chi-restraints excluded: chain J residue 759 LEU Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 822 LEU Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 901 ASP Chi-restraints excluded: chain J residue 906 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1142 ASN Chi-restraints excluded: chain J residue 1151 ASP Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1234 LYS Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 ASN J 355 ASN J 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120991 restraints weight = 26893.440| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.83 r_work: 0.3325 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14999 Z= 0.137 Angle : 0.614 9.963 20438 Z= 0.313 Chirality : 0.043 0.276 2190 Planarity : 0.004 0.051 2564 Dihedral : 11.308 104.717 2552 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.92 % Favored : 93.74 % Rotamer: Outliers : 6.78 % Allowed : 26.34 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 1741 helix: -0.90 (0.27), residues: 269 sheet: -1.23 (0.26), residues: 356 loop : -1.42 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 493 TYR 0.021 0.001 TYR J 833 PHE 0.032 0.001 PHE J 781 TRP 0.020 0.001 TRP A 491 HIS 0.004 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00302 (14943) covalent geometry : angle 0.59748 (20302) SS BOND : bond 0.00317 ( 32) SS BOND : angle 1.22473 ( 64) hydrogen bonds : bond 0.05036 ( 377) hydrogen bonds : angle 6.22468 ( 1058) link_ALPHA1-2 : bond 0.00906 ( 3) link_ALPHA1-2 : angle 1.68981 ( 9) link_ALPHA1-3 : bond 0.01059 ( 4) link_ALPHA1-3 : angle 2.30004 ( 12) link_ALPHA1-6 : bond 0.00472 ( 3) link_ALPHA1-6 : angle 1.60150 ( 9) link_BETA1-4 : bond 0.00560 ( 5) link_BETA1-4 : angle 3.09541 ( 15) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 2.10352 ( 3) link_NAG-ASN : bond 0.00382 ( 8) link_NAG-ASN : angle 1.97406 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 158 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 352 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 361 GLU cc_start: 0.6558 (mm-30) cc_final: 0.5862 (pt0) REVERT: A 366 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5508 (tp) REVERT: A 382 SER cc_start: 0.5643 (OUTLIER) cc_final: 0.4936 (t) REVERT: A 410 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6729 (t80) REVERT: A 531 MET cc_start: 0.8616 (ttt) cc_final: 0.8323 (ptm) REVERT: B 404 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: J 77 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7636 (mtp-110) REVERT: J 116 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8246 (t70) REVERT: J 134 LYS cc_start: 0.7991 (tppt) cc_final: 0.7509 (ttmt) REVERT: J 141 LYS cc_start: 0.8324 (mppt) cc_final: 0.8039 (mmmt) REVERT: J 292 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8020 (ptt-90) REVERT: J 363 ASP cc_start: 0.8492 (m-30) cc_final: 0.8093 (t0) REVERT: J 440 ILE cc_start: 0.6835 (mm) cc_final: 0.6503 (mm) REVERT: J 485 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7770 (mmtm) REVERT: J 596 HIS cc_start: 0.6593 (t70) cc_final: 0.6280 (t70) REVERT: J 735 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8661 (t80) REVERT: J 833 TYR cc_start: 0.8742 (t80) cc_final: 0.8506 (t80) REVERT: J 886 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7926 (tptp) REVERT: J 965 TYR cc_start: 0.7165 (m-10) cc_final: 0.6807 (m-80) REVERT: J 1031 TRP cc_start: 0.6264 (OUTLIER) cc_final: 0.5862 (m100) REVERT: J 1101 ARG cc_start: 0.4598 (OUTLIER) cc_final: 0.3256 (pmt-80) REVERT: J 1214 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7794 (mtm180) outliers start: 106 outliers final: 60 residues processed: 246 average time/residue: 0.1181 time to fit residues: 43.0072 Evaluate side-chains 213 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 139 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 209 ASP Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 360 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 485 LYS Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 733 ILE Chi-restraints excluded: chain J residue 735 PHE Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 GLN J 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123307 restraints weight = 18999.959| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.29 r_work: 0.3430 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14999 Z= 0.110 Angle : 0.573 9.758 20438 Z= 0.289 Chirality : 0.042 0.284 2190 Planarity : 0.004 0.046 2564 Dihedral : 9.971 97.039 2488 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.09 % Favored : 93.62 % Rotamer: Outliers : 6.01 % Allowed : 27.17 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.19), residues: 1741 helix: 0.23 (0.30), residues: 269 sheet: -1.24 (0.26), residues: 378 loop : -1.25 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J1222 TYR 0.018 0.001 TYR J 833 PHE 0.030 0.001 PHE J 781 TRP 0.011 0.001 TRP A 491 HIS 0.003 0.000 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00248 (14943) covalent geometry : angle 0.55657 (20302) SS BOND : bond 0.00296 ( 32) SS BOND : angle 1.10086 ( 64) hydrogen bonds : bond 0.03803 ( 377) hydrogen bonds : angle 5.62485 ( 1058) link_ALPHA1-2 : bond 0.00881 ( 3) link_ALPHA1-2 : angle 1.68336 ( 9) link_ALPHA1-3 : bond 0.01124 ( 4) link_ALPHA1-3 : angle 2.32745 ( 12) link_ALPHA1-6 : bond 0.00567 ( 3) link_ALPHA1-6 : angle 1.68998 ( 9) link_BETA1-4 : bond 0.00526 ( 5) link_BETA1-4 : angle 3.08916 ( 15) link_BETA1-6 : bond 0.00053 ( 1) link_BETA1-6 : angle 1.81094 ( 3) link_NAG-ASN : bond 0.00395 ( 8) link_NAG-ASN : angle 1.86051 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 159 time to evaluate : 0.588 Fit side-chains REVERT: A 361 GLU cc_start: 0.6446 (mm-30) cc_final: 0.5730 (pt0) REVERT: A 366 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5531 (tp) REVERT: A 401 VAL cc_start: 0.5201 (OUTLIER) cc_final: 0.4834 (t) REVERT: A 410 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6744 (t80) REVERT: J 77 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7685 (mtp-110) REVERT: J 116 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8295 (t70) REVERT: J 134 LYS cc_start: 0.7990 (tppt) cc_final: 0.7530 (ttmt) REVERT: J 141 LYS cc_start: 0.8366 (mppt) cc_final: 0.8066 (mmmt) REVERT: J 363 ASP cc_start: 0.8662 (m-30) cc_final: 0.8160 (t0) REVERT: J 440 ILE cc_start: 0.6725 (mm) cc_final: 0.6473 (mm) REVERT: J 596 HIS cc_start: 0.6711 (t70) cc_final: 0.6413 (t70) REVERT: J 735 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8753 (t80) REVERT: J 833 TYR cc_start: 0.8687 (t80) cc_final: 0.8312 (t80) REVERT: J 844 MET cc_start: 0.8200 (mmt) cc_final: 0.7729 (mmt) REVERT: J 886 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7866 (tptp) REVERT: J 958 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6904 (mtpp) REVERT: J 965 TYR cc_start: 0.7081 (m-10) cc_final: 0.6676 (m-80) REVERT: J 978 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.7139 (m-70) REVERT: J 1031 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.5940 (m100) REVERT: J 1101 ARG cc_start: 0.4681 (OUTLIER) cc_final: 0.3513 (ptm-80) REVERT: J 1346 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6890 (mp) outliers start: 94 outliers final: 68 residues processed: 235 average time/residue: 0.1409 time to fit residues: 48.4967 Evaluate side-chains 228 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 148 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 193 ASP Chi-restraints excluded: chain J residue 209 ASP Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 360 GLU Chi-restraints excluded: chain J residue 371 ARG Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 735 PHE Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 978 HIS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN J 481 HIS J 784 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117952 restraints weight = 21480.834| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.71 r_work: 0.3355 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14999 Z= 0.162 Angle : 0.592 9.998 20438 Z= 0.298 Chirality : 0.043 0.302 2190 Planarity : 0.004 0.049 2564 Dihedral : 9.470 89.486 2474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.26 % Favored : 93.45 % Rotamer: Outliers : 6.84 % Allowed : 26.73 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1741 helix: 0.73 (0.32), residues: 270 sheet: -1.22 (0.26), residues: 380 loop : -1.20 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.016 0.001 TYR J 833 PHE 0.034 0.001 PHE J 781 TRP 0.014 0.001 TRP A 491 HIS 0.004 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00376 (14943) covalent geometry : angle 0.57450 (20302) SS BOND : bond 0.00387 ( 32) SS BOND : angle 1.26442 ( 64) hydrogen bonds : bond 0.03557 ( 377) hydrogen bonds : angle 5.37703 ( 1058) link_ALPHA1-2 : bond 0.00811 ( 3) link_ALPHA1-2 : angle 1.73400 ( 9) link_ALPHA1-3 : bond 0.01072 ( 4) link_ALPHA1-3 : angle 2.47971 ( 12) link_ALPHA1-6 : bond 0.00455 ( 3) link_ALPHA1-6 : angle 1.73378 ( 9) link_BETA1-4 : bond 0.00415 ( 5) link_BETA1-4 : angle 3.06932 ( 15) link_BETA1-6 : bond 0.00137 ( 1) link_BETA1-6 : angle 1.71536 ( 3) link_NAG-ASN : bond 0.00361 ( 8) link_NAG-ASN : angle 1.84554 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 160 time to evaluate : 0.600 Fit side-chains REVERT: A 361 GLU cc_start: 0.6641 (mm-30) cc_final: 0.5976 (pt0) REVERT: A 366 LEU cc_start: 0.5868 (mt) cc_final: 0.5536 (tp) REVERT: A 401 VAL cc_start: 0.5227 (OUTLIER) cc_final: 0.4855 (t) REVERT: A 410 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6739 (t80) REVERT: B 391 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7621 (tttp) REVERT: B 512 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: J 77 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7773 (mtp-110) REVERT: J 116 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8369 (t70) REVERT: J 141 LYS cc_start: 0.8413 (mppt) cc_final: 0.8093 (mmmt) REVERT: J 292 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8222 (ptt-90) REVERT: J 363 ASP cc_start: 0.8722 (m-30) cc_final: 0.8209 (t0) REVERT: J 440 ILE cc_start: 0.6626 (mm) cc_final: 0.6393 (mm) REVERT: J 596 HIS cc_start: 0.6793 (t70) cc_final: 0.6464 (t70) REVERT: J 735 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.8708 (t80) REVERT: J 844 MET cc_start: 0.8400 (mmt) cc_final: 0.7867 (mmt) REVERT: J 886 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7848 (tptp) REVERT: J 978 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7225 (m-70) REVERT: J 1101 ARG cc_start: 0.4730 (OUTLIER) cc_final: 0.3609 (ptt90) REVERT: J 1214 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7881 (mtm180) REVERT: J 1278 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.8181 (ttp-110) REVERT: J 1346 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (mp) outliers start: 107 outliers final: 69 residues processed: 249 average time/residue: 0.1415 time to fit residues: 51.1701 Evaluate side-chains 224 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 143 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 209 ASP Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 735 PHE Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 978 HIS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS B 434 GLN J 81 ASN J 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.152359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118802 restraints weight = 21411.118| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.67 r_work: 0.3353 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14999 Z= 0.249 Angle : 0.652 10.059 20438 Z= 0.328 Chirality : 0.045 0.326 2190 Planarity : 0.004 0.051 2564 Dihedral : 9.512 82.284 2471 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.78 % Favored : 92.93 % Rotamer: Outliers : 7.16 % Allowed : 26.34 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 1741 helix: 0.75 (0.32), residues: 271 sheet: -1.38 (0.26), residues: 374 loop : -1.17 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.023 0.002 TYR J 833 PHE 0.038 0.002 PHE J 781 TRP 0.020 0.001 TRP A 491 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00582 (14943) covalent geometry : angle 0.63438 (20302) SS BOND : bond 0.00624 ( 32) SS BOND : angle 1.47069 ( 64) hydrogen bonds : bond 0.03726 ( 377) hydrogen bonds : angle 5.46289 ( 1058) link_ALPHA1-2 : bond 0.00824 ( 3) link_ALPHA1-2 : angle 1.73435 ( 9) link_ALPHA1-3 : bond 0.01123 ( 4) link_ALPHA1-3 : angle 2.69534 ( 12) link_ALPHA1-6 : bond 0.00431 ( 3) link_ALPHA1-6 : angle 1.83589 ( 9) link_BETA1-4 : bond 0.00371 ( 5) link_BETA1-4 : angle 3.09661 ( 15) link_BETA1-6 : bond 0.00323 ( 1) link_BETA1-6 : angle 1.75940 ( 3) link_NAG-ASN : bond 0.00346 ( 8) link_NAG-ASN : angle 1.96690 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 143 time to evaluate : 0.693 Fit side-chains REVERT: A 366 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5651 (tp) REVERT: A 410 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6701 (t80) REVERT: B 512 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: J 77 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7885 (mtp-110) REVERT: J 116 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8392 (t70) REVERT: J 134 LYS cc_start: 0.8192 (tppt) cc_final: 0.7450 (ttpt) REVERT: J 141 LYS cc_start: 0.8425 (mppt) cc_final: 0.8103 (mmmt) REVERT: J 149 TYR cc_start: 0.8875 (t80) cc_final: 0.8673 (t80) REVERT: J 292 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8184 (ptt-90) REVERT: J 363 ASP cc_start: 0.8733 (m-30) cc_final: 0.8238 (t0) REVERT: J 440 ILE cc_start: 0.6723 (mm) cc_final: 0.6464 (mm) REVERT: J 635 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8463 (mppt) REVERT: J 735 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8753 (t80) REVERT: J 886 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7908 (tptp) REVERT: J 978 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7359 (m-70) REVERT: J 1101 ARG cc_start: 0.4465 (OUTLIER) cc_final: 0.3552 (ptt90) REVERT: J 1177 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8121 (p0) REVERT: J 1214 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8045 (mtm180) outliers start: 112 outliers final: 73 residues processed: 235 average time/residue: 0.1321 time to fit residues: 45.2314 Evaluate side-chains 218 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 132 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 209 ASP Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 339 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 637 MET Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 733 ILE Chi-restraints excluded: chain J residue 735 PHE Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 978 HIS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1249 VAL Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 110 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 114 optimal weight: 0.0570 chunk 109 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN J 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119916 restraints weight = 26876.344| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.01 r_work: 0.3316 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14999 Z= 0.117 Angle : 0.585 9.361 20438 Z= 0.293 Chirality : 0.042 0.301 2190 Planarity : 0.003 0.047 2564 Dihedral : 9.064 76.600 2469 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.15 % Favored : 93.56 % Rotamer: Outliers : 6.39 % Allowed : 26.92 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1741 helix: 1.12 (0.33), residues: 270 sheet: -1.30 (0.26), residues: 372 loop : -1.13 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.016 0.001 TYR J 833 PHE 0.029 0.001 PHE J 781 TRP 0.012 0.001 TRP J1170 HIS 0.003 0.000 HIS J1230 Details of bonding type rmsd covalent geometry : bond 0.00264 (14943) covalent geometry : angle 0.56804 (20302) SS BOND : bond 0.00324 ( 32) SS BOND : angle 1.19591 ( 64) hydrogen bonds : bond 0.03270 ( 377) hydrogen bonds : angle 5.23980 ( 1058) link_ALPHA1-2 : bond 0.00898 ( 3) link_ALPHA1-2 : angle 1.67527 ( 9) link_ALPHA1-3 : bond 0.01195 ( 4) link_ALPHA1-3 : angle 2.47593 ( 12) link_ALPHA1-6 : bond 0.00599 ( 3) link_ALPHA1-6 : angle 1.71235 ( 9) link_BETA1-4 : bond 0.00479 ( 5) link_BETA1-4 : angle 3.02184 ( 15) link_BETA1-6 : bond 0.00027 ( 1) link_BETA1-6 : angle 1.71265 ( 3) link_NAG-ASN : bond 0.00384 ( 8) link_NAG-ASN : angle 1.82974 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 150 time to evaluate : 0.499 Fit side-chains REVERT: A 366 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5538 (tp) REVERT: A 410 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6706 (t80) REVERT: B 382 SER cc_start: 0.5304 (OUTLIER) cc_final: 0.5087 (t) REVERT: B 512 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: J 77 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7645 (mtp-110) REVERT: J 116 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8267 (t70) REVERT: J 141 LYS cc_start: 0.8337 (mppt) cc_final: 0.8010 (mmmt) REVERT: J 149 TYR cc_start: 0.8721 (t80) cc_final: 0.8509 (t80) REVERT: J 154 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7357 (mt-10) REVERT: J 292 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7958 (ptt-90) REVERT: J 363 ASP cc_start: 0.8617 (m-30) cc_final: 0.8134 (t0) REVERT: J 596 HIS cc_start: 0.6749 (t70) cc_final: 0.6447 (t70) REVERT: J 635 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8284 (mppt) REVERT: J 833 TYR cc_start: 0.8652 (t80) cc_final: 0.8309 (t80) REVERT: J 844 MET cc_start: 0.8341 (mmt) cc_final: 0.7843 (mmt) REVERT: J 886 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7718 (tptp) REVERT: J 978 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.7218 (m-70) REVERT: J 1101 ARG cc_start: 0.4447 (OUTLIER) cc_final: 0.3520 (ptt90) REVERT: J 1177 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8009 (p0) REVERT: J 1214 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: J 1346 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6941 (mp) outliers start: 100 outliers final: 68 residues processed: 235 average time/residue: 0.1287 time to fit residues: 44.3515 Evaluate side-chains 221 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 139 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 487 CYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 733 ILE Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 803 ASN Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 842 SER Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 978 HIS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1219 SER Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 89 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN J 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123662 restraints weight = 21903.205| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.26 r_work: 0.3346 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14999 Z= 0.199 Angle : 0.630 11.190 20438 Z= 0.314 Chirality : 0.044 0.313 2190 Planarity : 0.004 0.048 2564 Dihedral : 8.954 70.351 2466 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.72 % Favored : 92.99 % Rotamer: Outliers : 6.39 % Allowed : 27.30 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1741 helix: 1.10 (0.32), residues: 270 sheet: -1.34 (0.26), residues: 372 loop : -1.13 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 680 TYR 0.017 0.001 TYR J 833 PHE 0.036 0.002 PHE J 781 TRP 0.015 0.001 TRP A 491 HIS 0.003 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00469 (14943) covalent geometry : angle 0.61216 (20302) SS BOND : bond 0.00380 ( 32) SS BOND : angle 1.45022 ( 64) hydrogen bonds : bond 0.03505 ( 377) hydrogen bonds : angle 5.28598 ( 1058) link_ALPHA1-2 : bond 0.00809 ( 3) link_ALPHA1-2 : angle 1.69443 ( 9) link_ALPHA1-3 : bond 0.01279 ( 4) link_ALPHA1-3 : angle 2.72414 ( 12) link_ALPHA1-6 : bond 0.00494 ( 3) link_ALPHA1-6 : angle 1.79211 ( 9) link_BETA1-4 : bond 0.00393 ( 5) link_BETA1-4 : angle 3.07786 ( 15) link_BETA1-6 : bond 0.00190 ( 1) link_BETA1-6 : angle 1.70908 ( 3) link_NAG-ASN : bond 0.00326 ( 8) link_NAG-ASN : angle 1.86168 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 133 time to evaluate : 0.568 Fit side-chains REVERT: A 366 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5532 (tp) REVERT: A 410 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6731 (t80) REVERT: B 382 SER cc_start: 0.5498 (OUTLIER) cc_final: 0.5192 (t) REVERT: J 77 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7810 (mtp-110) REVERT: J 116 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (t70) REVERT: J 134 LYS cc_start: 0.8158 (tppt) cc_final: 0.7420 (ttpt) REVERT: J 141 LYS cc_start: 0.8354 (mppt) cc_final: 0.8045 (mmmt) REVERT: J 149 TYR cc_start: 0.8843 (t80) cc_final: 0.8632 (t80) REVERT: J 154 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7402 (mt-10) REVERT: J 292 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: J 363 ASP cc_start: 0.8664 (m-30) cc_final: 0.8191 (t0) REVERT: J 596 HIS cc_start: 0.6858 (t70) cc_final: 0.6545 (t70) REVERT: J 635 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8342 (mppt) REVERT: J 886 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7800 (tptp) REVERT: J 958 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7008 (mtpp) REVERT: J 978 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.7219 (m-70) REVERT: J 1101 ARG cc_start: 0.4508 (OUTLIER) cc_final: 0.3585 (ptt90) REVERT: J 1177 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8101 (p0) REVERT: J 1214 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7893 (mtm180) REVERT: J 1346 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6938 (mp) outliers start: 100 outliers final: 73 residues processed: 215 average time/residue: 0.1360 time to fit residues: 42.5390 Evaluate side-chains 218 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 131 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 487 CYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 637 MET Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 842 SER Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 978 HIS Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1219 SER Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.156991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124931 restraints weight = 23779.077| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.50 r_work: 0.3355 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14999 Z= 0.134 Angle : 0.599 9.683 20438 Z= 0.298 Chirality : 0.043 0.300 2190 Planarity : 0.004 0.046 2564 Dihedral : 8.769 65.714 2466 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.32 % Favored : 93.39 % Rotamer: Outliers : 5.82 % Allowed : 27.49 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1741 helix: 1.25 (0.33), residues: 270 sheet: -1.24 (0.26), residues: 378 loop : -1.12 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 680 TYR 0.016 0.001 TYR J 833 PHE 0.031 0.001 PHE J 781 TRP 0.014 0.001 TRP J 896 HIS 0.013 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00311 (14943) covalent geometry : angle 0.58107 (20302) SS BOND : bond 0.00302 ( 32) SS BOND : angle 1.36955 ( 64) hydrogen bonds : bond 0.03290 ( 377) hydrogen bonds : angle 5.21416 ( 1058) link_ALPHA1-2 : bond 0.00840 ( 3) link_ALPHA1-2 : angle 1.66300 ( 9) link_ALPHA1-3 : bond 0.01300 ( 4) link_ALPHA1-3 : angle 2.63971 ( 12) link_ALPHA1-6 : bond 0.00553 ( 3) link_ALPHA1-6 : angle 1.72120 ( 9) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 3.01049 ( 15) link_BETA1-6 : bond 0.00082 ( 1) link_BETA1-6 : angle 1.70872 ( 3) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 1.80173 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 141 time to evaluate : 0.584 Fit side-chains REVERT: A 410 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6750 (t80) REVERT: B 382 SER cc_start: 0.5487 (OUTLIER) cc_final: 0.5162 (t) REVERT: B 391 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7776 (tttp) REVERT: J 77 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7826 (mtp-110) REVERT: J 116 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8327 (t70) REVERT: J 134 LYS cc_start: 0.8230 (tppt) cc_final: 0.7511 (ttpt) REVERT: J 141 LYS cc_start: 0.8384 (mppt) cc_final: 0.8073 (mmmt) REVERT: J 154 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7465 (mt-10) REVERT: J 292 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: J 363 ASP cc_start: 0.8753 (m-30) cc_final: 0.8266 (t0) REVERT: J 596 HIS cc_start: 0.6955 (t70) cc_final: 0.6657 (t70) REVERT: J 635 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8303 (mppt) REVERT: J 886 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7790 (tptp) REVERT: J 958 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7027 (mtpp) REVERT: J 1101 ARG cc_start: 0.4455 (OUTLIER) cc_final: 0.3670 (ptt90) REVERT: J 1177 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8168 (p0) REVERT: J 1214 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7987 (mtm180) REVERT: J 1346 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6997 (mp) outliers start: 91 outliers final: 71 residues processed: 216 average time/residue: 0.1369 time to fit residues: 43.0624 Evaluate side-chains 218 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 135 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 487 CYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 842 SER Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1247 SER Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 135 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 559 GLN J 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.155262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119489 restraints weight = 29066.954| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.81 r_work: 0.3326 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14999 Z= 0.162 Angle : 0.610 9.408 20438 Z= 0.304 Chirality : 0.044 0.302 2190 Planarity : 0.004 0.047 2564 Dihedral : 8.615 62.038 2465 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.90 % Favored : 92.82 % Rotamer: Outliers : 5.75 % Allowed : 27.49 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1741 helix: 1.26 (0.33), residues: 270 sheet: -1.33 (0.26), residues: 372 loop : -1.11 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 493 TYR 0.023 0.001 TYR J 149 PHE 0.034 0.001 PHE J 781 TRP 0.015 0.001 TRP A 491 HIS 0.012 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00380 (14943) covalent geometry : angle 0.59236 (20302) SS BOND : bond 0.00335 ( 32) SS BOND : angle 1.38002 ( 64) hydrogen bonds : bond 0.03326 ( 377) hydrogen bonds : angle 5.21533 ( 1058) link_ALPHA1-2 : bond 0.00827 ( 3) link_ALPHA1-2 : angle 1.66977 ( 9) link_ALPHA1-3 : bond 0.01375 ( 4) link_ALPHA1-3 : angle 2.80008 ( 12) link_ALPHA1-6 : bond 0.00520 ( 3) link_ALPHA1-6 : angle 1.75684 ( 9) link_BETA1-4 : bond 0.00411 ( 5) link_BETA1-4 : angle 3.02660 ( 15) link_BETA1-6 : bond 0.00117 ( 1) link_BETA1-6 : angle 1.69281 ( 3) link_NAG-ASN : bond 0.00341 ( 8) link_NAG-ASN : angle 1.78977 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 138 time to evaluate : 0.689 Fit side-chains REVERT: A 410 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6719 (t80) REVERT: B 382 SER cc_start: 0.5221 (OUTLIER) cc_final: 0.4939 (t) REVERT: B 391 LYS cc_start: 0.8062 (ttpp) cc_final: 0.7619 (tttt) REVERT: J 77 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7620 (mtp-110) REVERT: J 116 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8249 (t70) REVERT: J 141 LYS cc_start: 0.8318 (mppt) cc_final: 0.8021 (mmmt) REVERT: J 150 MET cc_start: 0.8132 (tpp) cc_final: 0.7797 (mpp) REVERT: J 292 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7985 (ptt-90) REVERT: J 363 ASP cc_start: 0.8585 (m-30) cc_final: 0.8154 (t0) REVERT: J 442 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (p) REVERT: J 596 HIS cc_start: 0.6729 (t70) cc_final: 0.6435 (t70) REVERT: J 635 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8238 (mppt) REVERT: J 844 MET cc_start: 0.8425 (mmt) cc_final: 0.7903 (mmt) REVERT: J 886 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7657 (tptp) REVERT: J 958 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7005 (mtpp) REVERT: J 1101 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.3622 (ptt90) REVERT: J 1177 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8021 (p0) REVERT: J 1214 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7830 (mtm180) REVERT: J 1346 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7015 (mp) outliers start: 90 outliers final: 72 residues processed: 213 average time/residue: 0.1305 time to fit residues: 40.4992 Evaluate side-chains 220 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 135 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 487 CYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 928 VAL Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1247 SER Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN J 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124968 restraints weight = 19426.528| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.36 r_work: 0.3321 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14999 Z= 0.177 Angle : 0.620 9.461 20438 Z= 0.309 Chirality : 0.044 0.306 2190 Planarity : 0.004 0.047 2564 Dihedral : 8.599 61.941 2465 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.01 % Favored : 92.70 % Rotamer: Outliers : 5.88 % Allowed : 27.43 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1741 helix: 1.26 (0.33), residues: 270 sheet: -1.34 (0.26), residues: 372 loop : -1.12 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 493 TYR 0.016 0.001 TYR J 335 PHE 0.035 0.001 PHE J 781 TRP 0.015 0.001 TRP A 491 HIS 0.012 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00416 (14943) covalent geometry : angle 0.60174 (20302) SS BOND : bond 0.00339 ( 32) SS BOND : angle 1.36813 ( 64) hydrogen bonds : bond 0.03375 ( 377) hydrogen bonds : angle 5.21855 ( 1058) link_ALPHA1-2 : bond 0.00835 ( 3) link_ALPHA1-2 : angle 1.65425 ( 9) link_ALPHA1-3 : bond 0.01423 ( 4) link_ALPHA1-3 : angle 2.87269 ( 12) link_ALPHA1-6 : bond 0.00514 ( 3) link_ALPHA1-6 : angle 1.77216 ( 9) link_BETA1-4 : bond 0.00404 ( 5) link_BETA1-4 : angle 3.02592 ( 15) link_BETA1-6 : bond 0.00165 ( 1) link_BETA1-6 : angle 1.66544 ( 3) link_NAG-ASN : bond 0.00329 ( 8) link_NAG-ASN : angle 1.80976 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 136 time to evaluate : 0.561 Fit side-chains REVERT: A 410 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6669 (t80) REVERT: B 382 SER cc_start: 0.5549 (OUTLIER) cc_final: 0.5172 (t) REVERT: B 391 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7584 (tttt) REVERT: J 77 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7812 (mtp-110) REVERT: J 116 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8343 (t70) REVERT: J 134 LYS cc_start: 0.8194 (tppt) cc_final: 0.7497 (ttpt) REVERT: J 141 LYS cc_start: 0.8377 (mppt) cc_final: 0.8057 (mmmt) REVERT: J 154 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7592 (mt-10) REVERT: J 292 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8089 (ptt-90) REVERT: J 363 ASP cc_start: 0.8752 (m-30) cc_final: 0.8242 (t0) REVERT: J 442 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7861 (p) REVERT: J 596 HIS cc_start: 0.6905 (t70) cc_final: 0.6607 (t70) REVERT: J 635 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8302 (mppt) REVERT: J 844 MET cc_start: 0.8598 (mmt) cc_final: 0.8079 (mmt) REVERT: J 886 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7774 (tptp) REVERT: J 958 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7052 (mtpp) REVERT: J 1101 ARG cc_start: 0.4266 (OUTLIER) cc_final: 0.3750 (ptt90) REVERT: J 1177 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8189 (p0) REVERT: J 1214 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7970 (mtm180) REVERT: J 1346 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6980 (mp) outliers start: 92 outliers final: 76 residues processed: 212 average time/residue: 0.1325 time to fit residues: 40.8621 Evaluate side-chains 222 residues out of total 1564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 133 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 464 HIS Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain J residue 77 ARG Chi-restraints excluded: chain J residue 81 ASN Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 112 TRP Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 224 THR Chi-restraints excluded: chain J residue 235 CYS Chi-restraints excluded: chain J residue 292 ARG Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 452 VAL Chi-restraints excluded: chain J residue 456 TYR Chi-restraints excluded: chain J residue 461 GLU Chi-restraints excluded: chain J residue 473 VAL Chi-restraints excluded: chain J residue 486 LYS Chi-restraints excluded: chain J residue 487 CYS Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 635 LYS Chi-restraints excluded: chain J residue 639 LEU Chi-restraints excluded: chain J residue 671 LEU Chi-restraints excluded: chain J residue 726 THR Chi-restraints excluded: chain J residue 779 THR Chi-restraints excluded: chain J residue 785 CYS Chi-restraints excluded: chain J residue 794 LYS Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 828 THR Chi-restraints excluded: chain J residue 830 TRP Chi-restraints excluded: chain J residue 842 SER Chi-restraints excluded: chain J residue 883 PHE Chi-restraints excluded: chain J residue 886 LYS Chi-restraints excluded: chain J residue 914 ILE Chi-restraints excluded: chain J residue 915 SER Chi-restraints excluded: chain J residue 917 GLN Chi-restraints excluded: chain J residue 918 THR Chi-restraints excluded: chain J residue 927 THR Chi-restraints excluded: chain J residue 937 LYS Chi-restraints excluded: chain J residue 958 LYS Chi-restraints excluded: chain J residue 961 LEU Chi-restraints excluded: chain J residue 999 LEU Chi-restraints excluded: chain J residue 1031 TRP Chi-restraints excluded: chain J residue 1032 MET Chi-restraints excluded: chain J residue 1038 ARG Chi-restraints excluded: chain J residue 1058 VAL Chi-restraints excluded: chain J residue 1101 ARG Chi-restraints excluded: chain J residue 1161 ILE Chi-restraints excluded: chain J residue 1177 ASP Chi-restraints excluded: chain J residue 1209 MET Chi-restraints excluded: chain J residue 1214 ARG Chi-restraints excluded: chain J residue 1247 SER Chi-restraints excluded: chain J residue 1260 SER Chi-restraints excluded: chain J residue 1314 ILE Chi-restraints excluded: chain J residue 1317 VAL Chi-restraints excluded: chain J residue 1323 VAL Chi-restraints excluded: chain J residue 1327 ASP Chi-restraints excluded: chain J residue 1346 LEU Chi-restraints excluded: chain J residue 1358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 53 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 75 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN J 81 ASN J 803 ASN J 917 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118988 restraints weight = 23193.641| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.68 r_work: 0.3303 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14999 Z= 0.127 Angle : 0.597 9.643 20438 Z= 0.298 Chirality : 0.043 0.292 2190 Planarity : 0.004 0.046 2564 Dihedral : 8.494 60.813 2465 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.84 % Favored : 92.87 % Rotamer: Outliers : 5.88 % Allowed : 27.56 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1741 helix: 1.34 (0.33), residues: 271 sheet: -1.32 (0.26), residues: 374 loop : -1.10 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 493 TYR 0.013 0.001 TYR J 335 PHE 0.031 0.001 PHE J 781 TRP 0.013 0.001 TRP A 491 HIS 0.012 0.001 HIS J1345 Details of bonding type rmsd covalent geometry : bond 0.00292 (14943) covalent geometry : angle 0.58018 (20302) SS BOND : bond 0.00277 ( 32) SS BOND : angle 1.23537 ( 64) hydrogen bonds : bond 0.03258 ( 377) hydrogen bonds : angle 5.17885 ( 1058) link_ALPHA1-2 : bond 0.00831 ( 3) link_ALPHA1-2 : angle 1.65356 ( 9) link_ALPHA1-3 : bond 0.01434 ( 4) link_ALPHA1-3 : angle 2.77045 ( 12) link_ALPHA1-6 : bond 0.00571 ( 3) link_ALPHA1-6 : angle 1.72902 ( 9) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 2.97209 ( 15) link_BETA1-6 : bond 0.00021 ( 1) link_BETA1-6 : angle 1.73927 ( 3) link_NAG-ASN : bond 0.00359 ( 8) link_NAG-ASN : angle 1.76553 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4141.06 seconds wall clock time: 71 minutes 46.40 seconds (4306.40 seconds total)