Starting phenix.real_space_refine on Sat May 24 07:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdr_45485/05_2025/9cdr_45485_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdr_45485/05_2025/9cdr_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_2025/9cdr_45485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2025/9cdr_45485.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2025/9cdr_45485_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdr_45485/05_2025/9cdr_45485_neut_trim.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.93, per 1000 atoms: 0.44 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: 6.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.16 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: 9.63 Time building geometry restraints manager: 7.56 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=" 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 bond pdb=" C LEU B 449 " pdb=" N LYS B 450 " ideal model delta sigma weight residual 1.325 1.337 -0.012 1.25e-02 6.40e+03 9.89e-01 bond pdb=" CA PHE A 198 " pdb=" C PHE A 198 " ideal model delta sigma weight residual 1.534 1.525 0.009 9.50e-03 1.11e+04 9.71e-01 ... (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 806 or resid 901 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: 1.430 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: 0.380 Extract box with map and model: 0.800 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 50.340 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.930 ------------------------------------------------------------------------------- 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= 0.157 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 : 11.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (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 TRP 0.010 0.001 TRP A 798 HIS 0.004 0.001 HIS A 670 PHE 0.021 0.001 PHE A 602 TYR 0.017 0.001 TYR A 526 ARG 0.004 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.11360 ( 637) hydrogen bonds : angle 6.23939 ( 1854) covalent geometry : bond 0.00273 (12872) covalent geometry : angle 0.65032 (17464) 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 : 1.847 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: 0.6378 time to fit residues: 150.2285 Evaluate side-chains 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS A 634 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 ASN ** 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 543 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.065292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047597 restraints weight = 264963.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.049470 restraints weight = 146350.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.050653 restraints weight = 98389.765| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 12874 Z= 0.209 Angle : 0.620 7.407 17464 Z= 0.332 Chirality : 0.042 0.387 1930 Planarity : 0.005 0.071 2272 Dihedral : 5.956 68.231 1714 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 0.66 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1570 helix: 0.35 (0.19), residues: 679 sheet: -1.69 (0.28), residues: 311 loop : -1.22 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 327 HIS 0.006 0.001 HIS B 379 PHE 0.023 0.001 PHE A 602 TYR 0.019 0.001 TYR A 526 ARG 0.004 0.001 ARG A 696 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 637) hydrogen bonds : angle 5.65410 ( 1854) covalent geometry : bond 0.00417 (12872) covalent geometry : angle 0.62024 (17464) Misc. bond : bond 0.14707 ( 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 123 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.771 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: A 31 MET cc_start: 0.4325 (tpp) cc_final: 0.1971 (tpp) REVERT: A 281 GLU cc_start: 0.9098 (mp0) cc_final: 0.8728 (mp0) REVERT: A 453 GLN cc_start: 0.8791 (mt0) cc_final: 0.8089 (mm-40) REVERT: A 524 MET cc_start: 0.8900 (tmm) cc_final: 0.8556 (tmm) REVERT: B 374 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.9052 (tm-30) REVERT: B 456 CYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8249 (t) outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 0.5617 time to fit residues: 96.9587 Evaluate side-chains 112 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 A residue 667 ILE Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 374 GLU 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 135 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 626 GLN ** 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 536 GLN B 543 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.063404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046091 restraints weight = 268551.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.047861 restraints weight = 144851.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.049031 restraints weight = 97035.838| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 12874 Z= 0.251 Angle : 0.642 10.809 17464 Z= 0.344 Chirality : 0.041 0.389 1930 Planarity : 0.004 0.046 2272 Dihedral : 5.937 63.046 1714 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.83 % Favored : 91.91 % Rotamer: Outliers : 1.24 % Allowed : 14.13 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1570 helix: 0.37 (0.20), residues: 661 sheet: -1.77 (0.28), residues: 316 loop : -1.34 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 327 HIS 0.006 0.001 HIS B 298 PHE 0.023 0.002 PHE A 602 TYR 0.020 0.001 TYR A 526 ARG 0.005 0.001 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 637) hydrogen bonds : angle 5.62142 ( 1854) covalent geometry : bond 0.00491 (12872) covalent geometry : angle 0.64189 (17464) Misc. bond : bond 0.11884 ( 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 121 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.932 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: A 281 GLU cc_start: 0.9174 (mp0) cc_final: 0.8715 (mp0) REVERT: A 470 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8810 (m-40) REVERT: A 524 MET cc_start: 0.8894 (tmm) cc_final: 0.8570 (tmm) REVERT: B 456 CYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8438 (t) outliers start: 17 outliers final: 10 residues processed: 116 average time/residue: 0.5469 time to fit residues: 93.1295 Evaluate side-chains 113 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 700 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 0.3980 chunk 104 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 47 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- 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 ** 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 782 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 = 0.3775 r_free = 0.3775 target = 0.064772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047753 restraints weight = 263030.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049614 restraints weight = 139233.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.050828 restraints weight = 91512.560| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 12874 Z= 0.114 Angle : 0.570 6.784 17464 Z= 0.294 Chirality : 0.042 0.371 1930 Planarity : 0.004 0.045 2272 Dihedral : 5.752 64.678 1714 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 0.81 % Allowed : 14.13 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1570 helix: 0.70 (0.20), residues: 684 sheet: -1.59 (0.28), residues: 309 loop : -1.18 (0.28), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS B 298 PHE 0.021 0.001 PHE A 602 TYR 0.016 0.001 TYR A 526 ARG 0.002 0.000 ARG B 155 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 637) hydrogen bonds : angle 5.26191 ( 1854) covalent geometry : bond 0.00250 (12872) covalent geometry : angle 0.56962 (17464) Misc. bond : bond 0.08815 ( 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 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.933 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: A 281 GLU cc_start: 0.9177 (mp0) cc_final: 0.8661 (mp0) REVERT: A 413 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8314 (m) REVERT: A 524 MET cc_start: 0.8916 (tmm) cc_final: 0.8667 (tmm) REVERT: A 769 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9143 (mt0) REVERT: B 456 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8415 (t) REVERT: B 682 MET cc_start: 0.7296 (mtm) cc_final: 0.6865 (mtp) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.5707 time to fit residues: 90.5279 Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET 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 769 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 115 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 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 536 GLN ** 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 = 0.3737 r_free = 0.3737 target = 0.062906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.045839 restraints weight = 266441.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.047585 restraints weight = 143771.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.048770 restraints weight = 95867.378| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12874 Z= 0.209 Angle : 0.600 7.471 17464 Z= 0.318 Chirality : 0.041 0.392 1930 Planarity : 0.004 0.045 2272 Dihedral : 5.731 62.830 1714 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.97 % Rotamer: Outliers : 1.24 % Allowed : 14.49 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1570 helix: 0.64 (0.20), residues: 680 sheet: -1.65 (0.28), residues: 320 loop : -1.25 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 327 HIS 0.004 0.001 HIS A 311 PHE 0.022 0.001 PHE A 602 TYR 0.018 0.001 TYR A 526 ARG 0.004 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 637) hydrogen bonds : angle 5.34066 ( 1854) covalent geometry : bond 0.00413 (12872) covalent geometry : angle 0.59968 (17464) Misc. bond : bond 0.08331 ( 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: 17 poor density : 100 time to evaluate : 1.824 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: A 281 GLU cc_start: 0.9242 (mp0) cc_final: 0.8710 (mp0) REVERT: A 413 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8017 (m) REVERT: A 491 MET cc_start: 0.8888 (tmm) cc_final: 0.8542 (tmm) REVERT: A 524 MET cc_start: 0.8862 (tmm) cc_final: 0.8476 (tmm) REVERT: A 681 MET cc_start: 0.7799 (tmm) cc_final: 0.7507 (tmm) REVERT: B 456 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 680 MET cc_start: 0.8407 (tpp) cc_final: 0.8186 (tpp) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.5730 time to fit residues: 92.6907 Evaluate side-chains 111 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET 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 711 PHE Chi-restraints excluded: chain B residue 252 THR 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 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 26 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 155 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** 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 = 0.3748 r_free = 0.3748 target = 0.063368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.046029 restraints weight = 263965.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047814 restraints weight = 143342.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.049020 restraints weight = 95069.277| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 12874 Z= 0.136 Angle : 0.562 6.857 17464 Z= 0.292 Chirality : 0.041 0.382 1930 Planarity : 0.004 0.043 2272 Dihedral : 5.656 63.973 1714 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.80 % Rotamer: Outliers : 1.32 % Allowed : 14.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1570 helix: 0.85 (0.20), residues: 688 sheet: -1.60 (0.28), residues: 329 loop : -1.27 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 327 HIS 0.003 0.001 HIS B 298 PHE 0.020 0.001 PHE A 602 TYR 0.016 0.001 TYR A 526 ARG 0.005 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 637) hydrogen bonds : angle 5.14760 ( 1854) covalent geometry : bond 0.00286 (12872) covalent geometry : angle 0.56202 (17464) Misc. bond : bond 0.08035 ( 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 114 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.896 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: 0.9286 (mp0) cc_final: 0.8780 (mp0) REVERT: A 413 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8092 (m) REVERT: A 524 MET cc_start: 0.8938 (tmm) cc_final: 0.8621 (tmm) REVERT: A 769 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9139 (mt0) REVERT: B 456 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8414 (t) REVERT: B 680 MET cc_start: 0.8307 (tpp) cc_final: 0.8045 (tpp) REVERT: B 772 MET cc_start: 0.8720 (ttp) cc_final: 0.8190 (ttt) outliers start: 18 outliers final: 11 residues processed: 109 average time/residue: 0.5551 time to fit residues: 87.8807 Evaluate side-chains 110 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET 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 306 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 769 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 124 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.0570 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- 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 ** 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 782 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 = 0.3765 r_free = 0.3765 target = 0.064097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.047190 restraints weight = 268725.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.049041 restraints weight = 142738.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050278 restraints weight = 93913.406| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 12874 Z= 0.108 Angle : 0.551 7.749 17464 Z= 0.282 Chirality : 0.041 0.378 1930 Planarity : 0.004 0.042 2272 Dihedral : 5.519 64.935 1714 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 1.17 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1570 helix: 1.12 (0.20), residues: 688 sheet: -1.51 (0.29), residues: 317 loop : -1.12 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 327 HIS 0.003 0.001 HIS A 77 PHE 0.019 0.001 PHE A 602 TYR 0.015 0.001 TYR A 526 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 637) hydrogen bonds : angle 4.95657 ( 1854) covalent geometry : bond 0.00237 (12872) covalent geometry : angle 0.55139 (17464) Misc. bond : bond 0.07032 ( 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 112 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.816 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: 0.9322 (mp0) cc_final: 0.8908 (mp0) REVERT: A 413 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8092 (m) REVERT: A 524 MET cc_start: 0.8966 (tmm) cc_final: 0.8668 (tmm) REVERT: A 769 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9135 (mt0) REVERT: B 456 CYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 680 MET cc_start: 0.8205 (tpp) cc_final: 0.7895 (tpp) REVERT: B 772 MET cc_start: 0.8721 (ttp) cc_final: 0.8165 (ttt) outliers start: 16 outliers final: 11 residues processed: 108 average time/residue: 0.5896 time to fit residues: 91.7734 Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 111 THR 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 769 GLN 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 99 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 ** 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 = 0.3741 r_free = 0.3741 target = 0.062960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.045855 restraints weight = 265458.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.047621 restraints weight = 143320.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048804 restraints weight = 95670.304| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12874 Z= 0.158 Angle : 0.571 7.437 17464 Z= 0.296 Chirality : 0.040 0.389 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.482 63.404 1714 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.20 % Favored : 92.55 % Rotamer: Outliers : 1.24 % Allowed : 15.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1570 helix: 1.02 (0.20), residues: 695 sheet: -1.50 (0.28), residues: 319 loop : -1.21 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS B 152 PHE 0.020 0.001 PHE A 602 TYR 0.016 0.001 TYR A 526 ARG 0.003 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 637) hydrogen bonds : angle 5.00073 ( 1854) covalent geometry : bond 0.00323 (12872) covalent geometry : angle 0.57076 (17464) Misc. bond : bond 0.06951 ( 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 111 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.828 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: A 31 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.1905 (tpp) REVERT: A 281 GLU cc_start: 0.9304 (mp0) cc_final: 0.8779 (mp0) REVERT: A 413 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8089 (m) REVERT: A 524 MET cc_start: 0.8950 (tmm) cc_final: 0.8614 (tmm) REVERT: A 612 ILE cc_start: 0.8412 (mp) cc_final: 0.8118 (mp) REVERT: B 456 CYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8406 (t) REVERT: B 680 MET cc_start: 0.8229 (tpp) cc_final: 0.7902 (tpp) REVERT: B 772 MET cc_start: 0.8852 (ttp) cc_final: 0.8332 (ttt) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.5766 time to fit residues: 86.9592 Evaluate side-chains 109 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 111 THR 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 B residue 113 PHE Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 308 MET 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 119 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.062790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.045482 restraints weight = 266818.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.047297 restraints weight = 144203.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.048472 restraints weight = 95916.900| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 12874 Z= 0.145 Angle : 0.569 8.525 17464 Z= 0.293 Chirality : 0.041 0.387 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.476 63.054 1714 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 1.32 % Allowed : 15.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1570 helix: 1.05 (0.20), residues: 695 sheet: -1.54 (0.28), residues: 316 loop : -1.21 (0.29), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 327 HIS 0.003 0.001 HIS A 421 PHE 0.020 0.001 PHE A 602 TYR 0.016 0.001 TYR A 526 ARG 0.003 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 637) hydrogen bonds : angle 4.96661 ( 1854) covalent geometry : bond 0.00300 (12872) covalent geometry : angle 0.56854 (17464) Misc. bond : bond 0.06973 ( 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 115 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.880 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: A 31 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.1923 (tpp) REVERT: A 281 GLU cc_start: 0.9358 (mp0) cc_final: 0.8957 (mp0) REVERT: A 413 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8081 (m) REVERT: A 524 MET cc_start: 0.8945 (tmm) cc_final: 0.8604 (tmm) REVERT: A 612 ILE cc_start: 0.8379 (mp) cc_final: 0.8076 (mp) REVERT: B 456 CYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 680 MET cc_start: 0.8215 (tpp) cc_final: 0.7809 (tpp) REVERT: B 772 MET cc_start: 0.8848 (ttp) cc_final: 0.8321 (ttt) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.5711 time to fit residues: 91.0368 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 : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 111 THR 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 B residue 113 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 0.0770 chunk 88 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- 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 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 = 0.3729 r_free = 0.3729 target = 0.062315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.045134 restraints weight = 269855.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.046909 restraints weight = 143640.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.048103 restraints weight = 95297.016| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12874 Z= 0.170 Angle : 0.589 9.633 17464 Z= 0.306 Chirality : 0.041 0.386 1930 Planarity : 0.004 0.040 2272 Dihedral : 5.491 62.026 1714 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 1.24 % Allowed : 15.59 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1570 helix: 0.95 (0.20), residues: 695 sheet: -1.54 (0.28), residues: 319 loop : -1.24 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 327 HIS 0.004 0.001 HIS B 152 PHE 0.021 0.001 PHE A 602 TYR 0.016 0.001 TYR A 526 ARG 0.004 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 637) hydrogen bonds : angle 5.03168 ( 1854) covalent geometry : bond 0.00346 (12872) covalent geometry : angle 0.58904 (17464) Misc. bond : bond 0.06681 ( 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 109 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.895 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: A 30 MET cc_start: 0.0333 (ptt) cc_final: -0.0854 (ptt) REVERT: A 31 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.2160 (tpp) REVERT: A 413 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 524 MET cc_start: 0.8879 (tmm) cc_final: 0.8519 (tmm) REVERT: A 769 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9159 (mt0) REVERT: B 456 CYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8513 (t) REVERT: B 634 ASN cc_start: 0.9155 (t0) cc_final: 0.8943 (p0) REVERT: B 680 MET cc_start: 0.8094 (tpp) cc_final: 0.7738 (tpp) REVERT: B 772 MET cc_start: 0.8878 (ttp) cc_final: 0.8334 (ttt) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.5624 time to fit residues: 84.3847 Evaluate side-chains 108 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 111 THR 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 113 PHE Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 308 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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 = 0.3747 r_free = 0.3747 target = 0.062981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.045871 restraints weight = 264286.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.047693 restraints weight = 142722.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.048826 restraints weight = 94861.025| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12874 Z= 0.112 Angle : 0.567 9.310 17464 Z= 0.288 Chirality : 0.041 0.380 1930 Planarity : 0.004 0.039 2272 Dihedral : 5.428 63.039 1714 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.24 % Favored : 93.57 % Rotamer: Outliers : 1.17 % Allowed : 15.67 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1570 helix: 1.17 (0.20), residues: 697 sheet: -1.58 (0.28), residues: 334 loop : -1.04 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 327 HIS 0.003 0.001 HIS B 365 PHE 0.019 0.001 PHE A 602 TYR 0.015 0.001 TYR A 526 ARG 0.003 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 637) hydrogen bonds : angle 4.86142 ( 1854) covalent geometry : bond 0.00246 (12872) covalent geometry : angle 0.56656 (17464) Misc. bond : bond 0.06588 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7346.62 seconds wall clock time: 127 minutes 30.45 seconds (7650.45 seconds total)