Starting phenix.real_space_refine on Thu Jun 12 05:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjz_38411/06_2025/8xjz_38411.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8635 2.51 5 N 2379 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13651 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6508 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 41, 'TRANS': 817} Chain breaks: 1 Chain: "B" Number of atoms: 6576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6576 Classifications: {'peptide': 867} Link IDs: {'PTRANS': 42, 'TRANS': 824} Chain breaks: 1 Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 437 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain breaks: 1 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 8.98, per 1000 atoms: 0.66 Number of scatterers: 13651 At special positions: 0 Unit cell: (98.118, 99.2082, 209.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2583 8.00 N 2379 7.00 C 8635 6.00 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=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.8 seconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 16 sheets defined 35.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.660A pdb=" N ALA A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.571A pdb=" N VAL A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 74 through 79 removed outlier: 4.282A pdb=" N PHE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 79' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.627A pdb=" N PHE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.935A pdb=" N ASP A 112 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.987A pdb=" N MET A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 164 removed outlier: 4.011A pdb=" N THR A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.513A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 190 " --> pdb=" O CYS A 186 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.791A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.958A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.665A pdb=" N THR A 349 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.850A pdb=" N THR A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.001A pdb=" N ALA A 439 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 440 " --> pdb=" O LEU A 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 436 through 440' Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.695A pdb=" N ALA A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.676A pdb=" N THR A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 551 removed outlier: 4.130A pdb=" N GLN A 549 " --> pdb=" O HIS A 545 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 551' Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.943A pdb=" N ALA A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.684A pdb=" N LEU A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.607A pdb=" N PHE A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 611 Processing helix chain 'A' and resid 626 through 636 removed outlier: 3.609A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 646 removed outlier: 4.304A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 656 removed outlier: 3.685A pdb=" N GLN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.603A pdb=" N ALA A 674 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 675 " --> pdb=" O ILE A 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 671 through 675' Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 767 through 777 removed outlier: 4.305A pdb=" N TRP A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 806 through 811 Processing helix chain 'A' and resid 831 through 847 removed outlier: 4.177A pdb=" N LEU A 837 " --> pdb=" O HIS A 833 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.919A pdb=" N ALA A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 855 " --> pdb=" O LEU A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 855' Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.513A pdb=" N PHE B 77 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 105 removed outlier: 3.689A pdb=" N ARG B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.635A pdb=" N THR B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 192 removed outlier: 4.073A pdb=" N VAL B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN B 190 " --> pdb=" O CYS B 186 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 302 removed outlier: 3.671A pdb=" N ILE B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 333 removed outlier: 3.602A pdb=" N VAL B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.946A pdb=" N LYS B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.634A pdb=" N PHE B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.721A pdb=" N ALA B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 569 removed outlier: 3.735A pdb=" N ALA B 555 " --> pdb=" O TRP B 551 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.801A pdb=" N GLY B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 590 " --> pdb=" O GLN B 586 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 591 " --> pdb=" O GLY B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 614 removed outlier: 4.215A pdb=" N GLN B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.781A pdb=" N SER B 613 " --> pdb=" O GLN B 609 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 639 through 654 removed outlier: 3.728A pdb=" N ARG B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.570A pdb=" N ARG B 706 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 710 " --> pdb=" O ARG B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.595A pdb=" N GLU B 740 " --> pdb=" O ARG B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 777 removed outlier: 3.770A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 776 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 785 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 803 through 810 removed outlier: 3.894A pdb=" N ASN B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.584A pdb=" N ALA B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 884 Processing helix chain 'C' and resid 1495 through 1503 Processing helix chain 'C' and resid 1525 through 1538 removed outlier: 3.987A pdb=" N GLN C1529 " --> pdb=" O LEU C1525 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C1534 " --> pdb=" O MET C1530 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY C1535 " --> pdb=" O GLN C1531 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN C1536 " --> pdb=" O GLN C1532 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C1537 " --> pdb=" O TYR C1533 " (cutoff:3.500A) Processing helix chain 'C' and resid 1553 through 1562 Processing helix chain 'D' and resid 4 through 13 Processing helix chain 'D' and resid 18 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 172 removed outlier: 6.543A pdb=" N ILE A 119 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 203 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 248 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 249 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 265 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 428 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE A 270 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS A 426 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL A 272 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 424 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.538A pdb=" N LYS A 64 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 447 through 453 removed outlier: 3.562A pdb=" N SER A 447 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 519 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 661 through 665 removed outlier: 8.189A pdb=" N TYR A 690 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 685 " --> pdb=" O TYR A 690 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 692 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 694 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 681 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 779 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 797 removed outlier: 6.590A pdb=" N PHE A 796 " --> pdb=" O PHE A 820 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.786A pdb=" N ALA B 121 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.786A pdb=" N ALA B 121 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 247 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N MET B 13 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 249 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 265 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 428 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 270 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS B 426 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 429 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 413 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL B 311 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS B 342 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.888A pdb=" N LYS B 64 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB3, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AB4, first strand: chain 'B' and resid 447 through 448 removed outlier: 3.623A pdb=" N SER B 447 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=AB6, first strand: chain 'B' and resid 750 through 751 removed outlier: 4.036A pdb=" N THR B 750 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET B 621 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU B 529 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 620 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 530 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 799 " --> pdb=" O GLY B 530 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 532 " --> pdb=" O ILE B 799 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 663 through 665 removed outlier: 8.309A pdb=" N TYR B 690 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL B 685 " --> pdb=" O TYR B 690 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 692 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 681 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 779 " --> pdb=" O ALA B 683 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3933 1.33 - 1.46: 2826 1.46 - 1.58: 7096 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 13944 Sorted by residual: bond pdb=" C GLN B 597 " pdb=" N PRO B 598 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.23e-02 6.61e+03 1.46e+01 bond pdb=" N MET B 134 " pdb=" CA MET B 134 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.21e+01 bond pdb=" N VAL B 427 " pdb=" CA VAL B 427 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N VAL B 863 " pdb=" CA VAL B 863 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.14e+01 ... (remaining 13939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17852 2.38 - 4.77: 998 4.77 - 7.15: 106 7.15 - 9.54: 34 9.54 - 11.92: 5 Bond angle restraints: 18995 Sorted by residual: angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 110.70 119.74 -9.04 1.22e+00 6.72e-01 5.49e+01 angle pdb=" N THR A 484 " pdb=" CA THR A 484 " pdb=" C THR A 484 " ideal model delta sigma weight residual 114.56 106.16 8.40 1.27e+00 6.20e-01 4.37e+01 angle pdb=" N PHE A 558 " pdb=" CA PHE A 558 " pdb=" C PHE A 558 " ideal model delta sigma weight residual 111.82 104.93 6.89 1.16e+00 7.43e-01 3.53e+01 angle pdb=" N SER A 486 " pdb=" CA SER A 486 " pdb=" C SER A 486 " ideal model delta sigma weight residual 113.38 106.09 7.29 1.23e+00 6.61e-01 3.51e+01 angle pdb=" N ILE C1553 " pdb=" CA ILE C1553 " pdb=" C ILE C1553 " ideal model delta sigma weight residual 112.12 107.54 4.58 8.40e-01 1.42e+00 2.97e+01 ... (remaining 18990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7297 17.99 - 35.98: 751 35.98 - 53.97: 174 53.97 - 71.95: 41 71.95 - 89.94: 9 Dihedral angle restraints: 8272 sinusoidal: 3082 harmonic: 5190 Sorted by residual: dihedral pdb=" CA GLN B 24 " pdb=" C GLN B 24 " pdb=" N ALA B 25 " pdb=" CA ALA B 25 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA B 482 " pdb=" C ALA B 482 " pdb=" N TRP B 483 " pdb=" CA TRP B 483 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA UNK D 15 " pdb=" C UNK D 15 " pdb=" N UNK D 16 " pdb=" CA UNK D 16 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 8269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1812 0.095 - 0.189: 323 0.189 - 0.284: 30 0.284 - 0.378: 5 0.378 - 0.473: 4 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CB ILE B 201 " pdb=" CA ILE B 201 " pdb=" CG1 ILE B 201 " pdb=" CG2 ILE B 201 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CB ILE A 201 " pdb=" CA ILE A 201 " pdb=" CG1 ILE A 201 " pdb=" CG2 ILE A 201 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2171 not shown) Planarity restraints: 2489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 767 " -0.103 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 768 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO A 768 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 768 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 81 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 82 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 767 " 0.043 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 768 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 768 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 768 " 0.037 5.00e-02 4.00e+02 ... (remaining 2486 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2522 2.77 - 3.30: 11510 3.30 - 3.83: 21000 3.83 - 4.37: 24460 4.37 - 4.90: 43520 Nonbonded interactions: 103012 Sorted by model distance: nonbonded pdb=" OG SER B 181 " pdb=" O THR B 356 " model vdw 2.232 3.040 nonbonded pdb=" O PRO B 305 " pdb=" OH TYR B 341 " model vdw 2.240 3.040 nonbonded pdb=" O SER B 233 " pdb=" OG SER B 236 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR A 215 " pdb=" O ALA A 224 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 310 " pdb=" NZ LYS A 365 " model vdw 2.297 3.120 ... (remaining 103007 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' selection = (chain 'B' and (resid 6 through 134 or resid 153 through 882)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.640 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.011 0.103 13944 Z= 0.515 Angle : 1.212 11.922 18995 Z= 0.704 Chirality : 0.074 0.473 2174 Planarity : 0.009 0.152 2489 Dihedral : 16.051 89.942 4926 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.63 % Favored : 89.31 % Rotamer: Outliers : 4.30 % Allowed : 2.94 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.16), residues: 1768 helix: -3.40 (0.15), residues: 622 sheet: -2.56 (0.37), residues: 192 loop : -3.06 (0.16), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 629 HIS 0.009 0.002 HIS A 228 PHE 0.045 0.004 PHE B 26 TYR 0.022 0.004 TYR B 868 ARG 0.017 0.001 ARG B 489 Details of bonding type rmsd hydrogen bonds : bond 0.21072 ( 353) hydrogen bonds : angle 8.15678 ( 999) covalent geometry : bond 0.01079 (13944) covalent geometry : angle 1.21199 (18995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 144 time to evaluate : 1.400 Fit side-chains REVERT: A 275 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7259 (p0) REVERT: A 637 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (p) REVERT: A 663 LEU cc_start: 0.8094 (tp) cc_final: 0.7687 (tp) REVERT: B 423 THR cc_start: 0.6381 (OUTLIER) cc_final: 0.6138 (p) REVERT: B 542 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.3196 (ttm110) REVERT: B 728 MET cc_start: 0.4270 (mtt) cc_final: 0.3935 (mtt) REVERT: C 1538 CYS cc_start: 0.3309 (OUTLIER) cc_final: 0.2644 (t) outliers start: 60 outliers final: 7 residues processed: 181 average time/residue: 0.2451 time to fit residues: 66.2050 Evaluate side-chains 118 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain C residue 1538 CYS Chi-restraints excluded: chain C residue 1548 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 274 ASN A 314 HIS A 786 GLN B 56 GLN B 686 ASN B 883 GLN C1531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.182533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140962 restraints weight = 14483.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138211 restraints weight = 26660.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139946 restraints weight = 24798.870| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13944 Z= 0.117 Angle : 0.604 6.820 18995 Z= 0.316 Chirality : 0.043 0.151 2174 Planarity : 0.006 0.086 2489 Dihedral : 6.737 57.478 1954 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.51 % Allowed : 10.39 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.17), residues: 1768 helix: -2.56 (0.18), residues: 630 sheet: -1.55 (0.40), residues: 191 loop : -2.75 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1502 HIS 0.010 0.001 HIS C1541 PHE 0.018 0.001 PHE A 518 TYR 0.011 0.001 TYR A 128 ARG 0.003 0.000 ARG B 489 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 353) hydrogen bonds : angle 5.65085 ( 999) covalent geometry : bond 0.00269 (13944) covalent geometry : angle 0.60392 (18995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7574 (p0) REVERT: A 554 TYR cc_start: 0.8552 (t80) cc_final: 0.8337 (t80) REVERT: A 637 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7421 (p) REVERT: B 423 THR cc_start: 0.6060 (OUTLIER) cc_final: 0.5716 (p) REVERT: B 728 MET cc_start: 0.4158 (mtt) cc_final: 0.3742 (mtt) REVERT: C 1538 CYS cc_start: 0.3748 (OUTLIER) cc_final: 0.2789 (t) outliers start: 21 outliers final: 12 residues processed: 146 average time/residue: 0.2531 time to fit residues: 56.2592 Evaluate side-chains 133 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 1538 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 141 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 173 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 786 GLN B 228 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135534 restraints weight = 14752.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133490 restraints weight = 30240.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134549 restraints weight = 26455.131| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13944 Z= 0.224 Angle : 0.668 7.049 18995 Z= 0.350 Chirality : 0.047 0.215 2174 Planarity : 0.006 0.070 2489 Dihedral : 6.344 49.058 1944 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.87 % Allowed : 13.91 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.18), residues: 1768 helix: -2.14 (0.19), residues: 632 sheet: -1.73 (0.38), residues: 194 loop : -2.70 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1502 HIS 0.006 0.001 HIS C1541 PHE 0.026 0.002 PHE A 26 TYR 0.022 0.002 TYR B 875 ARG 0.011 0.001 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 353) hydrogen bonds : angle 5.48393 ( 999) covalent geometry : bond 0.00545 (13944) covalent geometry : angle 0.66760 (18995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8110 (t0) cc_final: 0.7879 (t0) REVERT: A 255 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 275 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7800 (p0) REVERT: B 728 MET cc_start: 0.4207 (mtt) cc_final: 0.3759 (mtt) outliers start: 40 outliers final: 23 residues processed: 144 average time/residue: 0.2442 time to fit residues: 53.2542 Evaluate side-chains 135 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 424 ASN Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 797 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.175891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.131835 restraints weight = 14642.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122873 restraints weight = 20987.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126582 restraints weight = 22040.413| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13944 Z= 0.180 Angle : 0.611 7.457 18995 Z= 0.318 Chirality : 0.045 0.236 2174 Planarity : 0.005 0.062 2489 Dihedral : 5.893 51.564 1940 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.15 % Allowed : 15.99 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.18), residues: 1768 helix: -1.87 (0.20), residues: 629 sheet: -1.64 (0.38), residues: 194 loop : -2.64 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1502 HIS 0.004 0.001 HIS C1541 PHE 0.022 0.002 PHE A 26 TYR 0.014 0.002 TYR A 868 ARG 0.005 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 353) hydrogen bonds : angle 5.24139 ( 999) covalent geometry : bond 0.00441 (13944) covalent geometry : angle 0.61127 (18995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 275 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7840 (p0) REVERT: A 554 TYR cc_start: 0.8569 (t80) cc_final: 0.8312 (t80) REVERT: A 637 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7490 (p) REVERT: B 526 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: B 600 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 649 ARG cc_start: 0.7773 (tpm170) cc_final: 0.7343 (tpm170) outliers start: 44 outliers final: 26 residues processed: 154 average time/residue: 0.2272 time to fit residues: 54.1612 Evaluate side-chains 144 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 775 MET Chi-restraints excluded: chain B residue 797 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 ASN B 350 ASN B 848 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134812 restraints weight = 14664.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130867 restraints weight = 29647.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133469 restraints weight = 25585.513| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13944 Z= 0.132 Angle : 0.555 7.003 18995 Z= 0.288 Chirality : 0.043 0.210 2174 Planarity : 0.005 0.057 2489 Dihedral : 5.538 50.804 1940 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.94 % Allowed : 17.85 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.19), residues: 1768 helix: -1.60 (0.21), residues: 624 sheet: -1.56 (0.39), residues: 190 loop : -2.50 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1502 HIS 0.007 0.001 HIS B 848 PHE 0.017 0.001 PHE A 26 TYR 0.010 0.001 TYR B 128 ARG 0.006 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 353) hydrogen bonds : angle 4.98096 ( 999) covalent geometry : bond 0.00318 (13944) covalent geometry : angle 0.55499 (18995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7813 (p0) REVERT: A 554 TYR cc_start: 0.8637 (t80) cc_final: 0.8319 (t80) REVERT: A 637 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7540 (p) REVERT: B 526 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: B 565 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5528 (tt) REVERT: B 600 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7986 (tt) outliers start: 41 outliers final: 26 residues processed: 150 average time/residue: 0.2412 time to fit residues: 55.6473 Evaluate side-chains 149 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 810 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN A 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.174398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132238 restraints weight = 14756.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130850 restraints weight = 35387.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133237 restraints weight = 24029.933| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13944 Z= 0.169 Angle : 0.590 7.218 18995 Z= 0.305 Chirality : 0.044 0.209 2174 Planarity : 0.005 0.056 2489 Dihedral : 5.550 53.919 1939 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.66 % Allowed : 17.71 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1768 helix: -1.50 (0.21), residues: 624 sheet: -1.43 (0.40), residues: 182 loop : -2.50 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A 228 PHE 0.021 0.002 PHE A 26 TYR 0.013 0.002 TYR A 868 ARG 0.007 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 353) hydrogen bonds : angle 4.99599 ( 999) covalent geometry : bond 0.00414 (13944) covalent geometry : angle 0.59028 (18995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 275 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 418 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 554 TYR cc_start: 0.8667 (t80) cc_final: 0.8395 (t80) REVERT: B 526 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: B 565 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5528 (tt) REVERT: B 600 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 649 ARG cc_start: 0.7468 (tpm170) cc_final: 0.7199 (tpm170) outliers start: 51 outliers final: 38 residues processed: 157 average time/residue: 0.2391 time to fit residues: 57.3350 Evaluate side-chains 158 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 818 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135617 restraints weight = 14900.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134193 restraints weight = 33542.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127445 restraints weight = 14922.319| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13944 Z= 0.208 Angle : 0.629 9.554 18995 Z= 0.324 Chirality : 0.046 0.221 2174 Planarity : 0.005 0.055 2489 Dihedral : 5.624 54.806 1937 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.37 % Allowed : 17.71 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1768 helix: -1.55 (0.21), residues: 623 sheet: -1.66 (0.38), residues: 197 loop : -2.51 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 629 HIS 0.004 0.001 HIS A 228 PHE 0.024 0.002 PHE A 26 TYR 0.016 0.002 TYR A 868 ARG 0.007 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 353) hydrogen bonds : angle 5.09555 ( 999) covalent geometry : bond 0.00512 (13944) covalent geometry : angle 0.62872 (18995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 110 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 275 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7810 (p0) REVERT: A 418 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 554 TYR cc_start: 0.8559 (t80) cc_final: 0.8334 (t80) REVERT: B 489 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6020 (mpt90) REVERT: B 526 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: B 565 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.5105 (tt) REVERT: B 600 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7868 (tt) REVERT: B 649 ARG cc_start: 0.7669 (tpm170) cc_final: 0.6905 (tpm170) REVERT: B 878 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5639 (m-30) REVERT: C 1549 ARG cc_start: 0.3528 (OUTLIER) cc_final: 0.2630 (mtm110) outliers start: 61 outliers final: 40 residues processed: 157 average time/residue: 0.2592 time to fit residues: 61.3848 Evaluate side-chains 156 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain C residue 1549 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 106 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 487 GLN A 786 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136514 restraints weight = 14687.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137573 restraints weight = 32096.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138861 restraints weight = 21674.422| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13944 Z= 0.107 Angle : 0.540 8.276 18995 Z= 0.275 Chirality : 0.042 0.187 2174 Planarity : 0.004 0.051 2489 Dihedral : 5.102 49.958 1937 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.94 % Allowed : 19.28 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1768 helix: -1.31 (0.21), residues: 624 sheet: -1.44 (0.39), residues: 189 loop : -2.33 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.003 0.000 HIS A 228 PHE 0.017 0.001 PHE A 781 TYR 0.009 0.001 TYR A 128 ARG 0.007 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 353) hydrogen bonds : angle 4.70374 ( 999) covalent geometry : bond 0.00256 (13944) covalent geometry : angle 0.53985 (18995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.565 Fit side-chains REVERT: A 199 MET cc_start: 0.9137 (ttt) cc_final: 0.8766 (ttt) REVERT: A 255 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 275 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7749 (p0) REVERT: B 489 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.6176 (mpt180) REVERT: B 526 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: B 565 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5584 (tt) REVERT: B 600 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 649 ARG cc_start: 0.7440 (tpm170) cc_final: 0.7188 (tpm170) outliers start: 41 outliers final: 29 residues processed: 153 average time/residue: 0.2564 time to fit residues: 58.7057 Evaluate side-chains 148 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 837 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 121 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 686 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141184 restraints weight = 14601.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139273 restraints weight = 28877.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140057 restraints weight = 24581.084| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13944 Z= 0.104 Angle : 0.534 8.350 18995 Z= 0.271 Chirality : 0.042 0.144 2174 Planarity : 0.004 0.051 2489 Dihedral : 4.893 48.199 1937 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.15 % Allowed : 19.50 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.19), residues: 1768 helix: -1.12 (0.21), residues: 617 sheet: -1.19 (0.38), residues: 198 loop : -2.25 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.003 0.000 HIS A 228 PHE 0.016 0.001 PHE A 26 TYR 0.009 0.001 TYR B 128 ARG 0.007 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02800 ( 353) hydrogen bonds : angle 4.57387 ( 999) covalent geometry : bond 0.00249 (13944) covalent geometry : angle 0.53369 (18995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 275 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 282 TYR cc_start: 0.8053 (t80) cc_final: 0.7756 (t80) REVERT: B 489 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.5898 (mpt180) REVERT: B 526 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: B 565 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5540 (tt) REVERT: B 600 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 649 ARG cc_start: 0.7362 (tpm170) cc_final: 0.7161 (tpm170) outliers start: 44 outliers final: 34 residues processed: 154 average time/residue: 0.2528 time to fit residues: 58.6122 Evaluate side-chains 159 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain C residue 1530 MET Chi-restraints excluded: chain C residue 1549 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 0.1980 chunk 55 optimal weight: 0.0060 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 487 GLN A 686 ASN B 686 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.181196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140436 restraints weight = 14450.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138004 restraints weight = 26798.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139677 restraints weight = 24323.787| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13944 Z= 0.093 Angle : 0.521 8.860 18995 Z= 0.264 Chirality : 0.041 0.142 2174 Planarity : 0.004 0.050 2489 Dihedral : 4.648 44.583 1937 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.72 % Allowed : 20.14 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.19), residues: 1768 helix: -0.90 (0.21), residues: 618 sheet: -1.03 (0.38), residues: 198 loop : -2.13 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.002 0.000 HIS A 228 PHE 0.014 0.001 PHE A 781 TYR 0.008 0.001 TYR A 396 ARG 0.007 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 353) hydrogen bonds : angle 4.39487 ( 999) covalent geometry : bond 0.00219 (13944) covalent geometry : angle 0.52135 (18995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 199 MET cc_start: 0.9145 (ttt) cc_final: 0.8786 (ttt) REVERT: A 255 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 275 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7658 (p0) REVERT: B 282 TYR cc_start: 0.8045 (t80) cc_final: 0.7755 (t80) REVERT: B 565 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5484 (tt) REVERT: C 1549 ARG cc_start: 0.3744 (OUTLIER) cc_final: 0.2464 (ttp-110) outliers start: 38 outliers final: 27 residues processed: 149 average time/residue: 0.2635 time to fit residues: 59.2748 Evaluate side-chains 153 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 793 ASP Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain C residue 1549 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 31 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 124 optimal weight: 0.4980 chunk 150 optimal weight: 0.0050 overall best weight: 0.3672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 686 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.182183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140115 restraints weight = 14512.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136862 restraints weight = 27334.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139158 restraints weight = 24523.342| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13944 Z= 0.090 Angle : 0.519 8.204 18995 Z= 0.262 Chirality : 0.041 0.142 2174 Planarity : 0.004 0.049 2489 Dihedral : 4.516 41.010 1937 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.51 % Allowed : 20.43 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.19), residues: 1768 helix: -0.76 (0.21), residues: 616 sheet: -0.95 (0.38), residues: 199 loop : -2.04 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 629 HIS 0.002 0.000 HIS A 228 PHE 0.013 0.001 PHE A 781 TYR 0.021 0.001 TYR A 540 ARG 0.006 0.000 ARG B 649 Details of bonding type rmsd hydrogen bonds : bond 0.02492 ( 353) hydrogen bonds : angle 4.30833 ( 999) covalent geometry : bond 0.00209 (13944) covalent geometry : angle 0.51906 (18995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3883.75 seconds wall clock time: 68 minutes 21.38 seconds (4101.38 seconds total)