Starting phenix.real_space_refine on Tue May 5 00:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2026/9cdr_45485_neut_trim.cif" } resolution = 3.91 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= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7990 2.51 5 N 2198 2.21 5 O 2348 1.98 5 H 12475 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s 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: 25079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12495 Classifications: {'peptide': 787} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751} Chain: "B" Number of atoms: 12494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12494 Classifications: {'peptide': 787} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 751} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.57, per 1000 atoms: 0.18 Number of scatterers: 25079 At special positions: 0 Unit cell: (88.7949, 103.325, 198.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2348 8.00 N 2198 7.00 C 7990 6.00 H 12475 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 981.4 milliseconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 49.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.931A pdb=" N LEU A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.695A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 133 through 153 removed outlier: 3.891A pdb=" N LEU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.563A pdb=" N ARG A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 352 through 380 removed outlier: 3.971A pdb=" N ARG A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 369 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 429 through 449 removed outlier: 4.447A pdb=" N TRP A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.784A pdb=" N LYS A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 539 through 563 removed outlier: 3.879A pdb=" N ASN A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 611 through 633 removed outlier: 3.617A pdb=" N GLY A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.816A pdb=" N GLN A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.853A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 740 through 756 removed outlier: 3.784A pdb=" N ILE A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 775 removed outlier: 3.520A pdb=" N LYS A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'B' and resid 21 through 28 removed outlier: 3.724A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.774A pdb=" N VAL B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.611A pdb=" N TYR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 87 " --> pdb=" O HIS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 133 through 152 removed outlier: 3.765A pdb=" N ILE B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 256 through 275 removed outlier: 3.693A pdb=" N SER B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 352 through 384 removed outlier: 3.530A pdb=" N LEU B 383 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.587A pdb=" N ASN B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 removed outlier: 3.685A pdb=" N ILE B 426 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 449 removed outlier: 4.238A pdb=" N GLN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.693A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 539 through 563 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.680A pdb=" N ILE B 603 " --> pdb=" O PRO B 599 " (cutoff:3.500A) Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 632 Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 653 through 664 removed outlier: 4.068A pdb=" N VAL B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 686 through 699 removed outlier: 4.054A pdb=" N GLN B 693 " --> pdb=" O PHE B 689 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 696 " --> pdb=" O ILE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 716 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.695A pdb=" N VAL B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 736 " --> pdb=" O VAL B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 755 removed outlier: 4.559A pdb=" N LEU B 744 " --> pdb=" O ARG B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.845A pdb=" N LYS B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 776 " --> pdb=" O MET B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.799A pdb=" N PHE A 44 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 99 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.789A pdb=" N SER A 254 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.500A pdb=" N ARG A 305 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N HIS A 311 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 303 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 313 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A 343 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 327 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS A 345 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 325 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 459 removed outlier: 5.125A pdb=" N ARG A 457 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 464 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 459 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE A 503 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.553A pdb=" N LEU A 640 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER A 641 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 583 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 580 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 574 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 582 " --> pdb=" O GLN A 572 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 566 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 780 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 168 removed outlier: 3.634A pdb=" N VAL B 167 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 223 through 224 removed outlier: 5.394A pdb=" N GLU B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.502A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 343 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 340 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.006A pdb=" N GLN B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 490 through 492 removed outlier: 3.503A pdb=" N ILE B 490 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 566 through 569 removed outlier: 3.534A pdb=" N ARG B 588 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN B 643 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 587 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU B 640 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU B 675 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 642 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 672 " --> pdb=" O GLY B 701 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER B 703 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 674 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 702 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 725 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 704 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 727 " --> pdb=" O VAL B 704 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR B 723 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 760 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU B 762 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 727 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLN B 782 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA B 761 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 781 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE B 573 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B 572 " --> pdb=" O TYR B 581 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1854 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: 7.29 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 12459 1.09 - 1.34: 4166 1.34 - 1.59: 8598 1.59 - 1.83: 116 1.83 - 2.08: 8 Bond restraints: 25347 Sorted by residual: bond pdb=" O1 OXY A 902 " pdb=" O2 OXY A 902 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O1 OXY B 902 " pdb=" O2 OXY B 902 " ideal model delta sigma weight residual 1.109 1.207 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N ILE A 256 " pdb=" CA ILE A 256 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.40e+00 bond pdb=" CA PHE A 198 " pdb=" CB PHE A 198 " ideal model delta sigma weight residual 1.525 1.534 -0.009 8.30e-03 1.45e+04 1.14e+00 bond pdb=" N VAL B 124 " pdb=" CA VAL B 124 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 ... (remaining 25342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 45860 7.13 - 14.25: 1 14.25 - 21.38: 0 21.38 - 28.50: 0 28.50 - 35.63: 3 Bond angle restraints: 45864 Sorted by residual: angle pdb=" N THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 110.00 74.37 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 109.00 74.40 34.60 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB THR A 257 " pdb=" CA THR A 257 " pdb=" HA THR A 257 " ideal model delta sigma weight residual 109.00 76.00 33.00 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N THR A 723 " pdb=" CA THR A 723 " pdb=" C THR A 723 " ideal model delta sigma weight residual 111.33 105.00 6.33 1.21e+00 6.83e-01 2.74e+01 angle pdb=" N GLU B 678 " pdb=" CA GLU B 678 " pdb=" C GLU B 678 " ideal model delta sigma weight residual 110.20 103.64 6.56 1.58e+00 4.01e-01 1.72e+01 ... (remaining 45859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10574 17.85 - 35.70: 907 35.70 - 53.55: 243 53.55 - 71.40: 77 71.40 - 89.25: 16 Dihedral angle restraints: 11817 sinusoidal: 6532 harmonic: 5285 Sorted by residual: dihedral pdb=" CA GLY B 227 " pdb=" C GLY B 227 " pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta harmonic sigma weight residual 180.00 -156.13 -23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA HIS B 648 " pdb=" C HIS B 648 " pdb=" N PHE B 649 " pdb=" CA PHE B 649 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA THR B 677 " pdb=" C THR B 677 " pdb=" N GLU B 678 " pdb=" CA GLU B 678 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 11814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1755 0.074 - 0.148: 173 0.148 - 0.222: 1 0.222 - 0.296: 0 0.296 - 0.370: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" CA THR A 257 " pdb=" N THR A 257 " pdb=" C THR A 257 " pdb=" CB THR A 257 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE A 583 " pdb=" N ILE A 583 " pdb=" C ILE A 583 " pdb=" CB ILE A 583 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1927 not shown) Planarity restraints: 3774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 597 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 598 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 696 " 0.152 9.50e-02 1.11e+02 5.07e-02 2.82e+00 pdb=" NE ARG A 696 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 696 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 696 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 696 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG A 696 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 696 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 696 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 696 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 539 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 540 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 540 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 540 " 0.021 5.00e-02 4.00e+02 ... (remaining 3771 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1118 2.16 - 2.77: 49419 2.77 - 3.38: 72429 3.38 - 3.99: 89538 3.99 - 4.60: 139250 Nonbonded interactions: 351754 Sorted by model distance: nonbonded pdb=" H THR A 257 " pdb=" HA THR A 257 " model vdw 1.546 1.816 nonbonded pdb=" OD1 ASN A 643 " pdb=" H SER A 645 " model vdw 1.571 2.450 nonbonded pdb=" HG1 THR A 766 " pdb=" OE1 GLN A 769 " model vdw 1.581 2.450 nonbonded pdb="HH21 ARG A 696 " pdb=" O VAL A 700 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASN B 512 " pdb=" H TYR B 515 " model vdw 1.590 2.450 ... (remaining 351749 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 20 through 589 or (resid 590 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 591 through 902)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.009 0.755 12874 Z= 0.169 Angle : 0.650 7.276 17464 Z= 0.434 Chirality : 0.041 0.370 1930 Planarity : 0.005 0.068 2272 Dihedral : 14.874 89.250 4810 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.37 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.93 (0.22), residues: 1570 helix: 0.40 (0.20), residues: 673 sheet: -1.56 (0.30), residues: 287 loop : -1.16 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 774 TYR 0.017 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.010 0.001 TRP A 798 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00299 (12872) covalent geometry : angle 0.65032 (17464) hydrogen bonds : bond 0.11360 ( 637) hydrogen bonds : angle 6.23939 ( 1854) Misc. bond : bond 0.69369 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3070 time to fit residues: 72.1202 Evaluate side-chains 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 306 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 HIS ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.066794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.049432 restraints weight = 256712.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.051426 restraints weight = 140115.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.052755 restraints weight = 90880.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.053643 restraints weight = 67113.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.054158 restraints weight = 54552.556| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 12874 Z= 0.137 Angle : 0.590 7.460 17464 Z= 0.311 Chirality : 0.042 0.376 1930 Planarity : 0.005 0.059 2272 Dihedral : 5.863 70.163 1714 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 0.51 % Allowed : 13.54 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.81 (0.22), residues: 1570 helix: 0.55 (0.20), residues: 673 sheet: -1.49 (0.29), residues: 299 loop : -1.15 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 716 TYR 0.017 0.001 TYR A 526 PHE 0.023 0.001 PHE A 602 TRP 0.013 0.001 TRP B 327 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00295 (12872) covalent geometry : angle 0.59020 (17464) hydrogen bonds : bond 0.03932 ( 637) hydrogen bonds : angle 5.53710 ( 1854) Misc. bond : bond 0.15702 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4605 (tpp) cc_final: 0.2032 (tpp) REVERT: A 281 GLU cc_start: 0.9059 (mp0) cc_final: 0.8692 (mp0) REVERT: A 357 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8925 (tp30) REVERT: A 453 GLN cc_start: 0.8771 (mt0) cc_final: 0.8317 (mm-40) REVERT: A 524 MET cc_start: 0.8850 (tmm) cc_final: 0.8530 (tmm) REVERT: B 456 CYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 682 MET cc_start: 0.7024 (mtm) cc_final: 0.6740 (mtp) outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.2749 time to fit residues: 47.9537 Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 456 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.065262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.047743 restraints weight = 265057.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.049600 restraints weight = 144396.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050742 restraints weight = 96345.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.051601 restraints weight = 73774.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052084 restraints weight = 61002.359| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12874 Z= 0.182 Angle : 0.593 7.525 17464 Z= 0.314 Chirality : 0.041 0.379 1930 Planarity : 0.004 0.045 2272 Dihedral : 5.768 66.893 1714 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 0.73 % Allowed : 13.98 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.89 (0.22), residues: 1570 helix: 0.61 (0.20), residues: 666 sheet: -1.68 (0.28), residues: 316 loop : -1.22 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 696 TYR 0.018 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.012 0.001 TRP B 327 HIS 0.005 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00368 (12872) covalent geometry : angle 0.59266 (17464) hydrogen bonds : bond 0.03921 ( 637) hydrogen bonds : angle 5.45625 ( 1854) Misc. bond : bond 0.11276 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9104 (mp0) cc_final: 0.8650 (mp0) REVERT: A 453 GLN cc_start: 0.8731 (mt0) cc_final: 0.8244 (mm-40) REVERT: A 524 MET cc_start: 0.8920 (tmm) cc_final: 0.8601 (tmm) REVERT: B 456 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8228 (t) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.2855 time to fit residues: 44.6763 Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 634 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.046332 restraints weight = 266145.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.048093 restraints weight = 143927.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049270 restraints weight = 96087.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.049988 restraints weight = 73380.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.050410 restraints weight = 61431.692| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 12874 Z= 0.212 Angle : 0.606 12.321 17464 Z= 0.322 Chirality : 0.041 0.389 1930 Planarity : 0.004 0.045 2272 Dihedral : 5.778 62.569 1714 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 1.24 % Allowed : 13.40 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.97 (0.22), residues: 1570 helix: 0.56 (0.20), residues: 677 sheet: -1.64 (0.28), residues: 319 loop : -1.36 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 131 TYR 0.019 0.001 TYR A 526 PHE 0.022 0.001 PHE A 602 TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00422 (12872) covalent geometry : angle 0.60640 (17464) hydrogen bonds : bond 0.03943 ( 637) hydrogen bonds : angle 5.45584 ( 1854) Misc. bond : bond 0.10117 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9195 (mp0) cc_final: 0.8711 (mp0) REVERT: A 413 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7935 (m) REVERT: A 524 MET cc_start: 0.8828 (tmm) cc_final: 0.8480 (tmm) REVERT: A 681 MET cc_start: 0.7713 (tmm) cc_final: 0.7098 (tmm) REVERT: B 456 CYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8429 (t) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.2865 time to fit residues: 44.9140 Evaluate side-chains 111 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.063359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.045836 restraints weight = 267180.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.047640 restraints weight = 145082.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048847 restraints weight = 95544.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.049630 restraints weight = 72426.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050071 restraints weight = 60346.428| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 12874 Z= 0.190 Angle : 0.598 8.226 17464 Z= 0.316 Chirality : 0.041 0.385 1930 Planarity : 0.004 0.046 2272 Dihedral : 5.760 62.202 1714 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.26 % Favored : 92.42 % Rotamer: Outliers : 1.39 % Allowed : 13.91 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.87 (0.22), residues: 1570 helix: 0.63 (0.20), residues: 676 sheet: -1.65 (0.28), residues: 318 loop : -1.25 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 716 TYR 0.018 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.013 0.001 TRP B 327 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00379 (12872) covalent geometry : angle 0.59818 (17464) hydrogen bonds : bond 0.03837 ( 637) hydrogen bonds : angle 5.36393 ( 1854) Misc. bond : bond 0.09105 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9263 (mp0) cc_final: 0.8725 (mp0) REVERT: A 413 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7817 (m) REVERT: A 470 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8791 (m-40) REVERT: A 524 MET cc_start: 0.8785 (tmm) cc_final: 0.8444 (tmm) REVERT: A 681 MET cc_start: 0.7671 (tmm) cc_final: 0.7173 (tmm) REVERT: A 769 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9154 (mt0) REVERT: B 456 CYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8422 (t) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.2834 time to fit residues: 45.0860 Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.063423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046026 restraints weight = 268108.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047807 restraints weight = 143713.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048980 restraints weight = 95693.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.049690 restraints weight = 73170.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050149 restraints weight = 60917.639| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 12874 Z= 0.150 Angle : 0.577 10.877 17464 Z= 0.300 Chirality : 0.041 0.382 1930 Planarity : 0.004 0.043 2272 Dihedral : 5.667 62.481 1714 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.26 % Favored : 92.48 % Rotamer: Outliers : 1.54 % Allowed : 14.42 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.75 (0.22), residues: 1570 helix: 0.79 (0.20), residues: 682 sheet: -1.63 (0.28), residues: 318 loop : -1.27 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.017 0.001 TYR A 526 PHE 0.020 0.001 PHE A 602 TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 663 Details of bonding type rmsd covalent geometry : bond 0.00310 (12872) covalent geometry : angle 0.57673 (17464) hydrogen bonds : bond 0.03621 ( 637) hydrogen bonds : angle 5.20288 ( 1854) Misc. bond : bond 0.08002 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.4948 (mmm) cc_final: 0.2544 (tpp) REVERT: A 281 GLU cc_start: 0.9276 (mp0) cc_final: 0.8780 (mp0) REVERT: A 413 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7867 (m) REVERT: A 524 MET cc_start: 0.8922 (tmm) cc_final: 0.8608 (tmm) REVERT: A 681 MET cc_start: 0.7660 (tmm) cc_final: 0.7288 (tmm) REVERT: A 769 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.9142 (mt0) REVERT: B 294 LEU cc_start: 0.8420 (mt) cc_final: 0.8138 (mp) REVERT: B 456 CYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8406 (t) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.2512 time to fit residues: 41.0116 Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.062870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.045727 restraints weight = 269369.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047460 restraints weight = 145170.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.048582 restraints weight = 97350.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.049307 restraints weight = 74289.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.049779 restraints weight = 62268.371| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12874 Z= 0.171 Angle : 0.576 6.960 17464 Z= 0.302 Chirality : 0.041 0.388 1930 Planarity : 0.004 0.043 2272 Dihedral : 5.622 61.685 1714 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.58 % Favored : 92.17 % Rotamer: Outliers : 1.24 % Allowed : 14.86 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.69 (0.22), residues: 1570 helix: 0.82 (0.20), residues: 685 sheet: -1.57 (0.28), residues: 321 loop : -1.24 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 774 TYR 0.017 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.010 0.001 TRP A 231 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00344 (12872) covalent geometry : angle 0.57639 (17464) hydrogen bonds : bond 0.03622 ( 637) hydrogen bonds : angle 5.16813 ( 1854) Misc. bond : bond 0.07418 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.5365 (mmm) cc_final: 0.2796 (tpp) REVERT: A 281 GLU cc_start: 0.9296 (mp0) cc_final: 0.8792 (mp0) REVERT: A 413 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7895 (m) REVERT: A 491 MET cc_start: 0.8885 (tmm) cc_final: 0.8498 (tmm) REVERT: A 524 MET cc_start: 0.8939 (tmm) cc_final: 0.8582 (tmm) REVERT: A 769 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9151 (mt0) REVERT: B 456 CYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 680 MET cc_start: 0.8111 (tpp) cc_final: 0.7826 (tpp) REVERT: B 772 MET cc_start: 0.8720 (ttp) cc_final: 0.8172 (ttt) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.2818 time to fit residues: 44.6517 Evaluate side-chains 109 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 617 ARG Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.062678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.045632 restraints weight = 267120.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047381 restraints weight = 143754.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048560 restraints weight = 95859.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.049234 restraints weight = 72871.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049742 restraints weight = 60360.724| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12874 Z= 0.162 Angle : 0.572 7.333 17464 Z= 0.299 Chirality : 0.041 0.387 1930 Planarity : 0.004 0.043 2272 Dihedral : 5.603 61.461 1714 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 1.24 % Allowed : 15.30 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.68 (0.22), residues: 1570 helix: 0.86 (0.20), residues: 684 sheet: -1.60 (0.28), residues: 318 loop : -1.26 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 716 TYR 0.016 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.010 0.001 TRP B 327 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00331 (12872) covalent geometry : angle 0.57196 (17464) hydrogen bonds : bond 0.03613 ( 637) hydrogen bonds : angle 5.13381 ( 1854) Misc. bond : bond 0.07429 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9351 (mp0) cc_final: 0.8829 (mp0) REVERT: A 413 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7741 (m) REVERT: A 524 MET cc_start: 0.8869 (tmm) cc_final: 0.8538 (tmm) REVERT: A 681 MET cc_start: 0.8021 (tmm) cc_final: 0.7600 (tmm) REVERT: A 769 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9156 (mt0) REVERT: B 456 CYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8517 (t) REVERT: B 772 MET cc_start: 0.8840 (ttp) cc_final: 0.8333 (ttt) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.2840 time to fit residues: 42.9498 Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 129 optimal weight: 0.0030 chunk 59 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.063843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.046956 restraints weight = 269247.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.048785 restraints weight = 142578.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050009 restraints weight = 93696.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050746 restraints weight = 70830.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.051261 restraints weight = 58138.572| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 12874 Z= 0.102 Angle : 0.558 8.552 17464 Z= 0.283 Chirality : 0.042 0.375 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.468 63.156 1714 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.43 % Favored : 93.31 % Rotamer: Outliers : 1.17 % Allowed : 15.52 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.32 (0.22), residues: 1570 helix: 1.21 (0.21), residues: 684 sheet: -1.42 (0.29), residues: 298 loop : -1.17 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.014 0.001 TYR A 526 PHE 0.019 0.001 PHE A 602 TRP 0.010 0.001 TRP A 231 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00232 (12872) covalent geometry : angle 0.55753 (17464) hydrogen bonds : bond 0.03225 ( 637) hydrogen bonds : angle 4.89862 ( 1854) Misc. bond : bond 0.05919 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9391 (mp0) cc_final: 0.8951 (mp0) REVERT: A 413 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7865 (m) REVERT: A 524 MET cc_start: 0.8925 (tmm) cc_final: 0.8666 (tmm) REVERT: A 612 ILE cc_start: 0.8333 (mp) cc_final: 0.8024 (mp) REVERT: A 681 MET cc_start: 0.8043 (tmm) cc_final: 0.7603 (tmm) REVERT: A 769 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9208 (mt0) REVERT: B 456 CYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8405 (t) REVERT: B 772 MET cc_start: 0.8818 (ttp) cc_final: 0.8285 (ttt) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.2786 time to fit residues: 44.7796 Evaluate side-chains 107 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.063036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.046053 restraints weight = 266757.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.047813 restraints weight = 143326.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.049028 restraints weight = 95195.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049799 restraints weight = 72034.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050247 restraints weight = 59609.820| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12874 Z= 0.140 Angle : 0.569 8.549 17464 Z= 0.294 Chirality : 0.041 0.386 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.423 61.667 1714 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 1.10 % Allowed : 15.67 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.37 (0.22), residues: 1570 helix: 1.16 (0.20), residues: 691 sheet: -1.49 (0.28), residues: 311 loop : -1.16 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.021 0.001 TYR A 80 PHE 0.020 0.001 PHE A 602 TRP 0.008 0.001 TRP A 798 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00292 (12872) covalent geometry : angle 0.56901 (17464) hydrogen bonds : bond 0.03355 ( 637) hydrogen bonds : angle 4.94419 ( 1854) Misc. bond : bond 0.06385 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.9328 (mp0) cc_final: 0.8781 (mp0) REVERT: A 413 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 524 MET cc_start: 0.8938 (tmm) cc_final: 0.8607 (tmm) REVERT: A 681 MET cc_start: 0.8490 (tmm) cc_final: 0.8096 (tmm) REVERT: A 769 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.9154 (mt0) REVERT: B 456 CYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 772 MET cc_start: 0.8848 (ttp) cc_final: 0.8355 (ttt) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.2934 time to fit residues: 44.3403 Evaluate side-chains 106 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 421 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 676 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.062608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.045648 restraints weight = 269938.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047435 restraints weight = 144482.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048631 restraints weight = 96037.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049315 restraints weight = 72837.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049799 restraints weight = 60249.048| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12874 Z= 0.139 Angle : 0.568 7.038 17464 Z= 0.293 Chirality : 0.041 0.385 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.414 60.506 1714 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 1.10 % Allowed : 15.45 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.38 (0.22), residues: 1570 helix: 1.15 (0.20), residues: 690 sheet: -1.55 (0.28), residues: 321 loop : -1.11 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.015 0.001 TYR A 526 PHE 0.021 0.001 PHE A 602 TRP 0.009 0.001 TRP A 798 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00290 (12872) covalent geometry : angle 0.56753 (17464) hydrogen bonds : bond 0.03353 ( 637) hydrogen bonds : angle 4.92590 ( 1854) Misc. bond : bond 0.05819 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.06 seconds wall clock time: 83 minutes 50.64 seconds (5030.64 seconds total)