Starting phenix.real_space_refine on Wed Mar 4 14:17:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n3v_48855/03_2026/9n3v_48855.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 7 Type Number sf(0) Gaussians Mg 5 5.21 5 S 84 5.16 5 Be 1 3.05 5 C 8806 2.51 5 N 2212 2.21 5 O 2572 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13683 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 32, 'TRANS': 856} Chain: "C" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 855} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' MG': 2, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.82, per 1000 atoms: 0.21 Number of scatterers: 13683 At special positions: 0 Unit cell: (107.88, 88.35, 220.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 84 16.00 Mg 5 11.99 F 3 9.00 O 2572 8.00 N 2212 7.00 C 8806 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 517.6 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 11 sheets defined 55.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.761A pdb=" N GLU A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.703A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.616A pdb=" N TYR A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 101 Processing helix chain 'A' and resid 102 through 105 removed outlier: 3.909A pdb=" N ALA A 105 " --> pdb=" O ILE A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.908A pdb=" N ILE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.829A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 303 through 317 removed outlier: 3.555A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.534A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.564A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.520A pdb=" N GLY A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 removed outlier: 3.583A pdb=" N TYR A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 removed outlier: 3.536A pdb=" N LYS A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.609A pdb=" N ALA A 456 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 457 " --> pdb=" O ASN A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 457' Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.510A pdb=" N MET A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 472' Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.544A pdb=" N ALA A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.570A pdb=" N THR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.738A pdb=" N ASP A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 595' Processing helix chain 'A' and resid 597 through 608 removed outlier: 3.924A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.602A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 676 through 713 removed outlier: 3.810A pdb=" N LYS A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 739 through 744 Proline residue: A 742 - end of helix No H-bonds generated for 'chain 'A' and resid 739 through 744' Processing helix chain 'A' and resid 758 through 769 Processing helix chain 'A' and resid 770 through 787 removed outlier: 3.592A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 794 removed outlier: 3.544A pdb=" N ALA A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 828 removed outlier: 3.601A pdb=" N MET A 822 " --> pdb=" O PHE A 818 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 828 " --> pdb=" O THR A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 879 through 906 removed outlier: 4.295A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 33 Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 84 through 102 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 268 through 300 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.571A pdb=" N THR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 339 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.235A pdb=" N ILE C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 397 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.063A pdb=" N THR C 457 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.888A pdb=" N GLU C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 547 through 558 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 589 through 595 Processing helix chain 'C' and resid 597 through 607 removed outlier: 3.596A pdb=" N ALA C 603 " --> pdb=" O ASN C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 629 Processing helix chain 'C' and resid 639 through 641 No H-bonds generated for 'chain 'C' and resid 639 through 641' Processing helix chain 'C' and resid 642 through 649 Processing helix chain 'C' and resid 659 through 665 Processing helix chain 'C' and resid 674 through 714 removed outlier: 3.702A pdb=" N LEU C 678 " --> pdb=" O ASP C 674 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 739 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 747 through 753 removed outlier: 4.617A pdb=" N VAL C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 787 Proline residue: C 771 - end of helix removed outlier: 4.336A pdb=" N PHE C 776 " --> pdb=" O THR C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 794 Processing helix chain 'C' and resid 795 through 799 Processing helix chain 'C' and resid 803 through 833 removed outlier: 3.979A pdb=" N ILE C 829 " --> pdb=" O GLN C 825 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS C 830 " --> pdb=" O THR C 826 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 862 Processing helix chain 'C' and resid 865 through 871 Processing helix chain 'C' and resid 879 through 901 removed outlier: 4.219A pdb=" N TRP C 883 " --> pdb=" O ASN C 879 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 893 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 894 " --> pdb=" O MET C 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176 removed outlier: 3.745A pdb=" N GLY A 242 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.816A pdb=" N LEU A 194 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.162A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 357 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET A 636 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS A 359 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 358 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 565 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR A 360 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 377 removed outlier: 4.382A pdb=" N MET A 374 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 534 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN A 514 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 536 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 512 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS A 450 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS A 432 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 377 removed outlier: 4.382A pdb=" N MET A 374 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA A 539 " --> pdb=" O MET A 374 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N HIS A 376 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR A 537 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 534 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY A 536 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 164 removed outlier: 4.559A pdb=" N ASN C 152 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 173 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 195 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 238 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C 193 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 240 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 191 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY C 242 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 189 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 244 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG C 187 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 194 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 159 through 164 removed outlier: 4.559A pdb=" N ASN C 152 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 173 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 195 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 238 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C 193 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 240 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 191 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY C 242 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 189 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL C 244 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG C 187 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.329A pdb=" N GLY C 652 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU C 670 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 654 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 633 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE C 653 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR C 635 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL C 655 " --> pdb=" O TYR C 635 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE C 357 " --> pdb=" O GLY C 634 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET C 636 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS C 359 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N PHE C 611 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE C 564 " --> pdb=" O PHE C 611 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 373 through 377 removed outlier: 3.969A pdb=" N LEU C 373 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 512 " --> pdb=" O MET C 535 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR C 537 " --> pdb=" O ILE C 510 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 510 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA C 539 " --> pdb=" O ARG C 508 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG C 508 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 446 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 435 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 373 through 377 removed outlier: 3.969A pdb=" N LEU C 373 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N MET C 532 " --> pdb=" O CYS C 475 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY C 536 " --> pdb=" O GLU C 479 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2151 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: 2.41 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2285 1.32 - 1.44: 3341 1.44 - 1.57: 8132 1.57 - 1.69: 1 1.69 - 1.82: 156 Bond restraints: 13915 Sorted by residual: bond pdb=" CA PHE A 269 " pdb=" C PHE A 269 " ideal model delta sigma weight residual 1.521 1.437 0.083 1.27e-02 6.20e+03 4.32e+01 bond pdb=" CA SER A 904 " pdb=" CB SER A 904 " ideal model delta sigma weight residual 1.536 1.439 0.097 1.53e-02 4.27e+03 4.01e+01 bond pdb=" CA SER A 821 " pdb=" CB SER A 821 " ideal model delta sigma weight residual 1.528 1.434 0.095 1.56e-02 4.11e+03 3.68e+01 bond pdb=" CA SER C 904 " pdb=" CB SER C 904 " ideal model delta sigma weight residual 1.537 1.457 0.080 1.38e-02 5.25e+03 3.37e+01 bond pdb=" C THR C 824 " pdb=" O THR C 824 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.15e-02 7.56e+03 1.50e+01 ... (remaining 13910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 18687 3.50 - 7.00: 135 7.00 - 10.51: 24 10.51 - 14.01: 6 14.01 - 17.51: 3 Bond angle restraints: 18855 Sorted by residual: angle pdb=" CA PHE A 269 " pdb=" CB PHE A 269 " pdb=" CG PHE A 269 " ideal model delta sigma weight residual 113.80 126.08 -12.28 1.00e+00 1.00e+00 1.51e+02 angle pdb=" C GLN A 825 " pdb=" CA GLN A 825 " pdb=" CB GLN A 825 " ideal model delta sigma weight residual 109.56 92.05 17.51 1.65e+00 3.67e-01 1.13e+02 angle pdb=" N THR A 268 " pdb=" CA THR A 268 " pdb=" CB THR A 268 " ideal model delta sigma weight residual 110.49 96.48 14.01 1.69e+00 3.50e-01 6.88e+01 angle pdb=" N ILE A 75 " pdb=" CA ILE A 75 " pdb=" C ILE A 75 " ideal model delta sigma weight residual 113.71 106.67 7.04 9.50e-01 1.11e+00 5.49e+01 angle pdb=" N PHE A 269 " pdb=" CA PHE A 269 " pdb=" C PHE A 269 " ideal model delta sigma weight residual 113.97 104.61 9.36 1.28e+00 6.10e-01 5.34e+01 ... (remaining 18850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7205 17.97 - 35.93: 936 35.93 - 53.90: 231 53.90 - 71.86: 46 71.86 - 89.83: 14 Dihedral angle restraints: 8432 sinusoidal: 3288 harmonic: 5144 Sorted by residual: dihedral pdb=" C GLN A 825 " pdb=" N GLN A 825 " pdb=" CA GLN A 825 " pdb=" CB GLN A 825 " ideal model delta harmonic sigma weight residual -122.60 -102.49 -20.11 0 2.50e+00 1.60e-01 6.47e+01 dihedral pdb=" C PHE A 269 " pdb=" N PHE A 269 " pdb=" CA PHE A 269 " pdb=" CB PHE A 269 " ideal model delta harmonic sigma weight residual -122.60 -103.67 -18.93 0 2.50e+00 1.60e-01 5.74e+01 dihedral pdb=" CD ARG A 187 " pdb=" NE ARG A 187 " pdb=" CZ ARG A 187 " pdb=" NH1 ARG A 187 " ideal model delta sinusoidal sigma weight residual 0.00 57.07 -57.07 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 8429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2106 0.083 - 0.167: 164 0.167 - 0.250: 9 0.250 - 0.334: 2 0.334 - 0.417: 1 Chirality restraints: 2282 Sorted by residual: chirality pdb=" CA PHE A 269 " pdb=" N PHE A 269 " pdb=" C PHE A 269 " pdb=" CB PHE A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA GLU A 908 " pdb=" N GLU A 908 " pdb=" C GLU A 908 " pdb=" CB GLU A 908 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 825 " pdb=" N GLN A 825 " pdb=" C GLN A 825 " pdb=" CB GLN A 825 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2279 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " -0.921 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG A 187 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 135 " -0.356 9.50e-02 1.11e+02 1.60e-01 1.56e+01 pdb=" NE ARG A 135 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 135 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 135 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 135 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 897 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C ILE C 897 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE C 897 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE C 898 " -0.019 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 58 2.43 - 3.05: 8930 3.05 - 3.66: 20983 3.66 - 4.28: 30880 4.28 - 4.90: 52185 Nonbonded interactions: 113036 Sorted by model distance: nonbonded pdb=" OD2 ASP A 361 " pdb="MG MG A1002 " model vdw 1.812 2.170 nonbonded pdb=" N GLU A 167 " pdb=" OE1 GLU A 167 " model vdw 1.958 3.120 nonbonded pdb=" OD1 ASN A 706 " pdb="MG MG A1001 " model vdw 1.971 2.170 nonbonded pdb=" O THR A 363 " pdb="MG MG A1002 " model vdw 2.034 2.170 nonbonded pdb=" OD1 ASN C 706 " pdb="MG MG C1003 " model vdw 2.048 2.170 ... (remaining 113031 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 22 through 1002) selection = (chain 'C' and resid 22 through 1002) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.920 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.006 0.478 13916 Z= 0.473 Angle : 0.793 17.509 18855 Z= 0.457 Chirality : 0.046 0.417 2282 Planarity : 0.010 0.413 2352 Dihedral : 17.297 89.826 5100 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.11 % Favored : 95.72 % Rotamer: Outliers : 2.62 % Allowed : 29.65 % Favored : 67.74 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1774 helix: 1.13 (0.18), residues: 895 sheet: -0.47 (0.37), residues: 172 loop : -1.00 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG A 443 TYR 0.012 0.001 TYR C 806 PHE 0.036 0.002 PHE A 269 TRP 0.009 0.001 TRP C 817 HIS 0.016 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00423 (13915) covalent geometry : angle 0.79296 (18855) hydrogen bonds : bond 0.13647 ( 722) hydrogen bonds : angle 5.83879 ( 2151) Misc. bond : bond 0.47778 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.3883 (OUTLIER) cc_final: 0.3127 (mmt90) REVERT: A 211 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7318 (mm) REVERT: A 231 MET cc_start: 0.6129 (ttt) cc_final: 0.5777 (ttp) REVERT: A 471 MET cc_start: 0.1316 (tmt) cc_final: 0.1009 (tpp) REVERT: A 535 MET cc_start: 0.3688 (ppp) cc_final: 0.1785 (ptp) REVERT: A 545 LYS cc_start: 0.7595 (pptt) cc_final: 0.6999 (ptmt) REVERT: A 656 ASP cc_start: 0.8242 (p0) cc_final: 0.7985 (p0) REVERT: C 40 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8745 (pp30) REVERT: C 47 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8031 (mtpm) REVERT: C 74 LEU cc_start: 0.8510 (mm) cc_final: 0.7962 (tp) REVERT: C 135 ARG cc_start: 0.7848 (mpt-90) cc_final: 0.7264 (mpt90) REVERT: C 255 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8578 (mp0) REVERT: C 256 MET cc_start: 0.9050 (mtm) cc_final: 0.8608 (ptp) REVERT: C 440 PHE cc_start: 0.8513 (m-80) cc_final: 0.8311 (m-10) REVERT: C 586 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8157 (mtpt) REVERT: C 647 LYS cc_start: 0.8796 (mttp) cc_final: 0.8491 (mtpm) REVERT: C 672 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 822 MET cc_start: 0.8961 (tpt) cc_final: 0.8739 (tpt) REVERT: C 874 MET cc_start: 0.8855 (ttm) cc_final: 0.8376 (ttm) outliers start: 40 outliers final: 24 residues processed: 154 average time/residue: 0.5770 time to fit residues: 96.9453 Evaluate side-chains 138 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 821 SER Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 739 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 745 ASN A 825 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073085 restraints weight = 22335.570| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.48 r_work: 0.2871 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13916 Z= 0.141 Angle : 0.585 11.142 18855 Z= 0.300 Chirality : 0.042 0.203 2282 Planarity : 0.004 0.050 2352 Dihedral : 6.082 54.296 1906 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.34 % Rotamer: Outliers : 4.38 % Allowed : 26.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1774 helix: 1.29 (0.18), residues: 921 sheet: -0.40 (0.37), residues: 170 loop : -1.13 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 443 TYR 0.021 0.002 TYR C 79 PHE 0.022 0.001 PHE A 438 TRP 0.009 0.001 TRP C 302 HIS 0.011 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00330 (13915) covalent geometry : angle 0.58474 (18855) hydrogen bonds : bond 0.04428 ( 722) hydrogen bonds : angle 4.60541 ( 2151) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 122 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.4912 (OUTLIER) cc_final: 0.4328 (mmt90) REVERT: A 231 MET cc_start: 0.5977 (ttt) cc_final: 0.5619 (ttp) REVERT: A 237 SER cc_start: 0.6616 (OUTLIER) cc_final: 0.6335 (p) REVERT: A 471 MET cc_start: 0.1370 (tmt) cc_final: 0.1136 (tpp) REVERT: A 505 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 507 MET cc_start: 0.6349 (mtp) cc_final: 0.6113 (mtp) REVERT: A 535 MET cc_start: 0.3902 (ppp) cc_final: 0.2395 (ptp) REVERT: A 545 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7024 (ptmt) REVERT: A 656 ASP cc_start: 0.8298 (p0) cc_final: 0.8076 (p0) REVERT: C 40 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8721 (pp30) REVERT: C 47 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8039 (mtpm) REVERT: C 74 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7721 (tp) REVERT: C 77 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7706 (mtp-110) REVERT: C 135 ARG cc_start: 0.7894 (mpt-90) cc_final: 0.7289 (mpt90) REVERT: C 181 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8360 (ttp) REVERT: C 256 MET cc_start: 0.9008 (mtm) cc_final: 0.8510 (ptp) REVERT: C 586 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8069 (mtpt) REVERT: C 672 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7899 (mm-30) REVERT: C 822 MET cc_start: 0.8998 (tpt) cc_final: 0.8718 (tpt) REVERT: C 874 MET cc_start: 0.8877 (ttm) cc_final: 0.8436 (ttm) outliers start: 67 outliers final: 25 residues processed: 178 average time/residue: 0.5221 time to fit residues: 102.3395 Evaluate side-chains 146 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 766 MET Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.126719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072805 restraints weight = 22390.867| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.46 r_work: 0.2862 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13916 Z= 0.142 Angle : 0.555 9.469 18855 Z= 0.286 Chirality : 0.042 0.216 2282 Planarity : 0.004 0.053 2352 Dihedral : 5.003 46.037 1875 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 4.65 % Allowed : 25.52 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1774 helix: 1.39 (0.18), residues: 915 sheet: -0.37 (0.37), residues: 170 loop : -1.08 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 443 TYR 0.015 0.001 TYR A 430 PHE 0.016 0.001 PHE A 283 TRP 0.010 0.001 TRP C 302 HIS 0.003 0.001 HIS A 726 Details of bonding type rmsd covalent geometry : bond 0.00338 (13915) covalent geometry : angle 0.55540 (18855) hydrogen bonds : bond 0.04190 ( 722) hydrogen bonds : angle 4.43902 ( 2151) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 118 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.4943 (OUTLIER) cc_final: 0.4649 (mmt180) REVERT: A 266 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8103 (mmmm) REVERT: A 390 HIS cc_start: 0.6967 (m90) cc_final: 0.6575 (m90) REVERT: A 471 MET cc_start: 0.1347 (tmt) cc_final: 0.1129 (tpp) REVERT: A 505 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 535 MET cc_start: 0.4448 (ppp) cc_final: 0.2600 (ptp) REVERT: A 545 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7037 (ptmt) REVERT: C 40 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8672 (pp30) REVERT: C 47 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7966 (mtpm) REVERT: C 74 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7732 (tp) REVERT: C 77 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7688 (mtp-110) REVERT: C 135 ARG cc_start: 0.7867 (mpt-90) cc_final: 0.7356 (mpt90) REVERT: C 181 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: C 255 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 256 MET cc_start: 0.8964 (mtm) cc_final: 0.8432 (ptp) REVERT: C 586 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8036 (mtpt) REVERT: C 672 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 822 MET cc_start: 0.9003 (tpt) cc_final: 0.8666 (tpt) REVERT: C 874 MET cc_start: 0.8867 (ttm) cc_final: 0.8442 (ttm) outliers start: 71 outliers final: 29 residues processed: 179 average time/residue: 0.5479 time to fit residues: 107.6312 Evaluate side-chains 143 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 766 MET Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 852 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 514 GLN C 825 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072301 restraints weight = 22314.005| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.45 r_work: 0.2851 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13916 Z= 0.144 Angle : 0.557 11.952 18855 Z= 0.283 Chirality : 0.042 0.172 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.877 41.489 1873 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 4.65 % Allowed : 25.39 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1774 helix: 1.41 (0.18), residues: 919 sheet: -0.33 (0.38), residues: 170 loop : -1.15 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.023 0.001 TYR C 79 PHE 0.015 0.001 PHE A 283 TRP 0.011 0.001 TRP C 302 HIS 0.003 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00345 (13915) covalent geometry : angle 0.55658 (18855) hydrogen bonds : bond 0.04089 ( 722) hydrogen bonds : angle 4.33177 ( 2151) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 117 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8218 (mmmm) REVERT: A 505 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 535 MET cc_start: 0.4658 (ppp) cc_final: 0.3139 (ptp) REVERT: A 545 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7033 (ptmt) REVERT: A 773 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8272 (p) REVERT: C 40 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8611 (pp30) REVERT: C 47 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7976 (mtpm) REVERT: C 74 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7796 (tp) REVERT: C 77 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7631 (mtp-110) REVERT: C 135 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7277 (mpt90) REVERT: C 181 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: C 256 MET cc_start: 0.8937 (mtm) cc_final: 0.8441 (ptp) REVERT: C 586 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8021 (mtpt) REVERT: C 672 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7861 (mm-30) REVERT: C 822 MET cc_start: 0.9014 (tpt) cc_final: 0.8665 (tpt) REVERT: C 874 MET cc_start: 0.8863 (ttm) cc_final: 0.8437 (ttm) outliers start: 71 outliers final: 31 residues processed: 181 average time/residue: 0.5104 time to fit residues: 102.0875 Evaluate side-chains 144 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 766 MET Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 745 ASN C 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.069359 restraints weight = 22428.026| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.46 r_work: 0.2790 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13916 Z= 0.252 Angle : 0.616 10.721 18855 Z= 0.316 Chirality : 0.045 0.164 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.918 43.291 1868 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.32 % Rotamer: Outliers : 5.56 % Allowed : 24.41 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1774 helix: 1.17 (0.18), residues: 926 sheet: -0.53 (0.37), residues: 175 loop : -1.11 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 627 TYR 0.015 0.002 TYR C 806 PHE 0.020 0.002 PHE A 898 TRP 0.011 0.001 TRP C 302 HIS 0.010 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00622 (13915) covalent geometry : angle 0.61575 (18855) hydrogen bonds : bond 0.04932 ( 722) hydrogen bonds : angle 4.50321 ( 2151) Misc. bond : bond 0.00163 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 109 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8284 (mmmm) REVERT: A 505 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 535 MET cc_start: 0.4984 (ppp) cc_final: 0.3471 (ptp) REVERT: A 545 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7139 (ptmt) REVERT: A 773 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8356 (p) REVERT: C 40 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8730 (pp30) REVERT: C 43 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8718 (mmtm) REVERT: C 47 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8070 (mtpm) REVERT: C 77 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7746 (mtp-110) REVERT: C 135 ARG cc_start: 0.8027 (mpt-90) cc_final: 0.7467 (mpt90) REVERT: C 181 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8335 (ttp) REVERT: C 255 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 256 MET cc_start: 0.8946 (mtm) cc_final: 0.8423 (ptp) REVERT: C 497 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8395 (mtpt) REVERT: C 586 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8073 (mtpt) REVERT: C 650 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: C 672 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7910 (mm-30) REVERT: C 874 MET cc_start: 0.8879 (ttm) cc_final: 0.8482 (ttm) outliers start: 85 outliers final: 40 residues processed: 186 average time/residue: 0.4920 time to fit residues: 101.5190 Evaluate side-chains 152 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 744 ASP Chi-restraints excluded: chain C residue 766 MET Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 0.0170 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 161 optimal weight: 0.0470 chunk 135 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 825 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.127296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073699 restraints weight = 22338.986| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.46 r_work: 0.2857 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13916 Z= 0.106 Angle : 0.545 9.585 18855 Z= 0.280 Chirality : 0.041 0.174 2282 Planarity : 0.004 0.049 2352 Dihedral : 4.657 43.772 1868 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 2.95 % Allowed : 27.62 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1774 helix: 1.47 (0.18), residues: 916 sheet: -0.39 (0.37), residues: 175 loop : -1.09 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 686 TYR 0.024 0.001 TYR C 79 PHE 0.016 0.001 PHE C 818 TRP 0.012 0.001 TRP C 817 HIS 0.014 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00232 (13915) covalent geometry : angle 0.54532 (18855) hydrogen bonds : bond 0.03658 ( 722) hydrogen bonds : angle 4.23403 ( 2151) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8171 (mmmm) REVERT: A 505 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: A 535 MET cc_start: 0.4717 (ppp) cc_final: 0.3026 (ptp) REVERT: A 545 LYS cc_start: 0.7634 (pptt) cc_final: 0.7027 (ptmt) REVERT: A 656 ASP cc_start: 0.8435 (p0) cc_final: 0.8152 (p0) REVERT: A 825 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: C 40 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8599 (pp30) REVERT: C 43 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8686 (mmtm) REVERT: C 47 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7900 (mtpm) REVERT: C 77 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7585 (mtp-110) REVERT: C 135 ARG cc_start: 0.7857 (mpt-90) cc_final: 0.7378 (mpt90) REVERT: C 181 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8239 (ttp) REVERT: C 255 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8419 (mt-10) REVERT: C 256 MET cc_start: 0.8853 (mtm) cc_final: 0.8376 (ptp) REVERT: C 586 LYS cc_start: 0.8444 (mmmt) cc_final: 0.7930 (mtpt) REVERT: C 672 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7544 (mt-10) REVERT: C 874 MET cc_start: 0.8845 (ttm) cc_final: 0.8406 (ttm) outliers start: 45 outliers final: 13 residues processed: 158 average time/residue: 0.5680 time to fit residues: 98.3077 Evaluate side-chains 127 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 596 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 165 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 69 optimal weight: 0.0050 chunk 154 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN C 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.127385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074298 restraints weight = 22277.216| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.45 r_work: 0.2863 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13916 Z= 0.104 Angle : 0.547 10.233 18855 Z= 0.277 Chirality : 0.041 0.180 2282 Planarity : 0.004 0.065 2352 Dihedral : 4.588 47.661 1868 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.72 % Favored : 96.11 % Rotamer: Outliers : 2.75 % Allowed : 28.80 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1774 helix: 1.57 (0.18), residues: 914 sheet: -0.35 (0.38), residues: 175 loop : -1.07 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 443 TYR 0.011 0.001 TYR C 806 PHE 0.016 0.001 PHE C 818 TRP 0.011 0.001 TRP C 817 HIS 0.014 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00229 (13915) covalent geometry : angle 0.54698 (18855) hydrogen bonds : bond 0.03521 ( 722) hydrogen bonds : angle 4.19408 ( 2151) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.6065 (pp30) REVERT: A 231 MET cc_start: 0.6161 (ttt) cc_final: 0.5724 (ttp) REVERT: A 266 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8152 (mmmm) REVERT: A 505 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 535 MET cc_start: 0.4413 (ppp) cc_final: 0.2924 (ptp) REVERT: A 545 LYS cc_start: 0.7580 (pptt) cc_final: 0.6985 (ptmt) REVERT: A 656 ASP cc_start: 0.8452 (p0) cc_final: 0.8130 (p0) REVERT: C 40 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8610 (pp30) REVERT: C 43 LYS cc_start: 0.8890 (mmmm) cc_final: 0.8679 (mmtm) REVERT: C 47 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7939 (mtpm) REVERT: C 77 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7583 (mtp-110) REVERT: C 135 ARG cc_start: 0.7892 (mpt-90) cc_final: 0.7396 (mpt90) REVERT: C 181 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8219 (ttp) REVERT: C 255 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8401 (mt-10) REVERT: C 256 MET cc_start: 0.8829 (mtm) cc_final: 0.8347 (OUTLIER) REVERT: C 586 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7927 (mtpt) REVERT: C 650 ASP cc_start: 0.8389 (m-30) cc_final: 0.7935 (m-30) REVERT: C 672 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7511 (mt-10) REVERT: C 874 MET cc_start: 0.8848 (ttm) cc_final: 0.8448 (ttm) outliers start: 42 outliers final: 17 residues processed: 157 average time/residue: 0.5395 time to fit residues: 93.2357 Evaluate side-chains 132 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 376 HIS Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 517 ASN A 745 ASN C 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072780 restraints weight = 22248.511| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.47 r_work: 0.2832 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13916 Z= 0.142 Angle : 0.583 15.031 18855 Z= 0.292 Chirality : 0.042 0.178 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.288 40.800 1863 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 2.16 % Allowed : 29.65 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1774 helix: 1.54 (0.18), residues: 915 sheet: -0.33 (0.38), residues: 175 loop : -1.07 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 443 TYR 0.024 0.001 TYR C 79 PHE 0.015 0.001 PHE A 283 TRP 0.010 0.001 TRP C 302 HIS 0.013 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00346 (13915) covalent geometry : angle 0.58273 (18855) hydrogen bonds : bond 0.03853 ( 722) hydrogen bonds : angle 4.25229 ( 2151) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8030 (pt) REVERT: A 266 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8142 (mmmm) REVERT: A 505 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 535 MET cc_start: 0.4619 (ppp) cc_final: 0.3080 (ptp) REVERT: A 545 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7015 (ptmt) REVERT: A 656 ASP cc_start: 0.8409 (p0) cc_final: 0.8082 (p0) REVERT: C 40 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8595 (pp30) REVERT: C 47 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7940 (mtpm) REVERT: C 77 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7590 (mtp-110) REVERT: C 135 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7438 (mpt90) REVERT: C 181 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8207 (ttp) REVERT: C 255 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8406 (mt-10) REVERT: C 256 MET cc_start: 0.8817 (mtm) cc_final: 0.8370 (OUTLIER) REVERT: C 586 LYS cc_start: 0.8444 (mmmt) cc_final: 0.7925 (mtpt) REVERT: C 650 ASP cc_start: 0.8415 (m-30) cc_final: 0.7996 (m-30) REVERT: C 672 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7513 (mt-10) REVERT: C 874 MET cc_start: 0.8852 (ttm) cc_final: 0.8441 (ttm) outliers start: 33 outliers final: 16 residues processed: 138 average time/residue: 0.5497 time to fit residues: 83.4888 Evaluate side-chains 128 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 766 MET Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 745 ASN A 825 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.126776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073302 restraints weight = 22342.507| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.43 r_work: 0.2842 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13916 Z= 0.125 Angle : 0.590 15.814 18855 Z= 0.291 Chirality : 0.042 0.178 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.262 40.588 1863 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 2.42 % Allowed : 29.71 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1774 helix: 1.54 (0.18), residues: 916 sheet: -0.29 (0.38), residues: 175 loop : -1.05 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 443 TYR 0.024 0.001 TYR A 61 PHE 0.014 0.001 PHE C 818 TRP 0.010 0.001 TRP C 302 HIS 0.011 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00296 (13915) covalent geometry : angle 0.59030 (18855) hydrogen bonds : bond 0.03735 ( 722) hydrogen bonds : angle 4.23412 ( 2151) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7993 (pt) REVERT: A 231 MET cc_start: 0.6194 (ttt) cc_final: 0.5752 (ttp) REVERT: A 266 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8163 (mmmm) REVERT: A 505 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: A 535 MET cc_start: 0.4585 (ppp) cc_final: 0.2958 (ptp) REVERT: A 545 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7015 (ptmt) REVERT: A 656 ASP cc_start: 0.8371 (p0) cc_final: 0.8068 (p0) REVERT: A 773 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 825 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: C 40 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8597 (pp30) REVERT: C 47 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7949 (mtpm) REVERT: C 77 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7538 (mtp-110) REVERT: C 135 ARG cc_start: 0.7924 (mpt-90) cc_final: 0.7451 (mpt90) REVERT: C 181 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: C 255 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8406 (mt-10) REVERT: C 256 MET cc_start: 0.8786 (mtm) cc_final: 0.8355 (ptp) REVERT: C 586 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7911 (mtpt) REVERT: C 650 ASP cc_start: 0.8375 (m-30) cc_final: 0.7953 (m-30) REVERT: C 672 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7516 (mt-10) REVERT: C 874 MET cc_start: 0.8848 (ttm) cc_final: 0.8446 (ttm) outliers start: 37 outliers final: 18 residues processed: 142 average time/residue: 0.5597 time to fit residues: 87.0893 Evaluate side-chains 134 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 745 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073707 restraints weight = 22287.345| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.43 r_work: 0.2851 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13916 Z= 0.117 Angle : 0.592 15.755 18855 Z= 0.291 Chirality : 0.042 0.179 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.243 40.257 1863 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 1.90 % Allowed : 29.97 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1774 helix: 1.56 (0.18), residues: 916 sheet: -0.26 (0.38), residues: 175 loop : -1.03 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 443 TYR 0.024 0.001 TYR C 79 PHE 0.014 0.001 PHE C 818 TRP 0.011 0.001 TRP C 817 HIS 0.010 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00275 (13915) covalent geometry : angle 0.59186 (18855) hydrogen bonds : bond 0.03647 ( 722) hydrogen bonds : angle 4.21802 ( 2151) Misc. bond : bond 0.00034 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8052 (pt) REVERT: A 231 MET cc_start: 0.6142 (ttt) cc_final: 0.5707 (ttp) REVERT: A 266 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8111 (mmmm) REVERT: A 505 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 535 MET cc_start: 0.4495 (ppp) cc_final: 0.2863 (ptp) REVERT: A 545 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6996 (ptmt) REVERT: A 656 ASP cc_start: 0.8293 (p0) cc_final: 0.7977 (p0) REVERT: A 773 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 40 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8571 (pp30) REVERT: C 47 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7938 (mtpm) REVERT: C 77 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7540 (mtp-110) REVERT: C 135 ARG cc_start: 0.7932 (mpt-90) cc_final: 0.7444 (mpt90) REVERT: C 181 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: C 255 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8381 (mt-10) REVERT: C 256 MET cc_start: 0.8790 (mtm) cc_final: 0.8351 (ptp) REVERT: C 586 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7870 (mtpt) REVERT: C 650 ASP cc_start: 0.8364 (m-30) cc_final: 0.7956 (m-30) REVERT: C 672 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7522 (mt-10) REVERT: C 874 MET cc_start: 0.8854 (ttm) cc_final: 0.8460 (ttm) REVERT: C 908 GLU cc_start: 0.8109 (pm20) cc_final: 0.7759 (pm20) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.5636 time to fit residues: 84.3010 Evaluate side-chains 134 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.0010 chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN ** C 53 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 = 0.3872 r_free = 0.3872 target = 0.127042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073612 restraints weight = 22537.462| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.45 r_work: 0.2848 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.347 13916 Z= 0.161 Angle : 0.804 59.132 18855 Z= 0.442 Chirality : 0.043 0.464 2282 Planarity : 0.004 0.050 2352 Dihedral : 4.271 40.254 1863 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.78 % Favored : 96.00 % Rotamer: Outliers : 1.96 % Allowed : 29.84 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1774 helix: 1.57 (0.18), residues: 916 sheet: -0.26 (0.38), residues: 175 loop : -1.04 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 443 TYR 0.016 0.001 TYR A 61 PHE 0.014 0.001 PHE C 818 TRP 0.011 0.001 TRP C 817 HIS 0.009 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00434 (13915) covalent geometry : angle 0.80396 (18855) hydrogen bonds : bond 0.03657 ( 722) hydrogen bonds : angle 4.23202 ( 2151) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6358.95 seconds wall clock time: 108 minutes 41.82 seconds (6521.82 seconds total)