Starting phenix.real_space_refine on Wed Mar 4 09:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dgd_30671/03_2026/7dgd_30671.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 98 5.16 5 C 7958 2.51 5 N 2074 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 34, 'TRANS': 751} Chain breaks: 1 Chain: "B" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6187 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 751} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.19, per 1000 atoms: 0.26 Number of scatterers: 12381 At special positions: 0 Unit cell: (119.85, 95.88, 186.12, 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 98 16.00 O 2251 8.00 N 2074 7.00 C 7958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 291 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 544 " distance=2.04 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 394 " distance=2.04 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 562 " distance=2.05 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 746 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 661.4 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 46.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.886A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.469A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 4.010A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.563A pdb=" N LEU A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.719A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.954A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.037A pdb=" N GLU A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.690A pdb=" N ALA A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 4.102A pdb=" N ASP A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 357 No H-bonds generated for 'chain 'A' and resid 356 through 357' Processing helix chain 'A' and resid 358 through 362 removed outlier: 4.004A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 422 removed outlier: 4.054A pdb=" N ILE A 414 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.911A pdb=" N HIS A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 removed outlier: 4.065A pdb=" N ASP A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 removed outlier: 4.001A pdb=" N THR A 576 " --> pdb=" O ALA A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 593 through 615 removed outlier: 3.616A pdb=" N ILE A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'A' and resid 627 through 649 removed outlier: 4.305A pdb=" N CYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Proline residue: A 645 - end of helix removed outlier: 3.799A pdb=" N ILE A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 689 removed outlier: 3.563A pdb=" N SER A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 4.299A pdb=" N LEU A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 removed outlier: 4.310A pdb=" N GLN A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.662A pdb=" N VAL A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Proline residue: A 756 - end of helix Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.910A pdb=" N ARG A 775 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 808 removed outlier: 3.790A pdb=" N TYR A 786 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A 802 " --> pdb=" O TRP A 798 " (cutoff:3.500A) Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 810 through 837 removed outlier: 4.024A pdb=" N THR A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 833 - end of helix Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.597A pdb=" N VAL B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.765A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.626A pdb=" N LEU B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.711A pdb=" N VAL B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.790A pdb=" N ASP B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 409 through 431 removed outlier: 4.019A pdb=" N ILE B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 572 through 576 removed outlier: 4.061A pdb=" N THR B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 613 removed outlier: 4.038A pdb=" N ALA B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 649 removed outlier: 4.064A pdb=" N CYS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 635 " --> pdb=" O CYS B 631 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) Proline residue: B 645 - end of helix removed outlier: 3.801A pdb=" N ILE B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 689 removed outlier: 4.409A pdb=" N SER B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 682 " --> pdb=" O LYS B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 726 removed outlier: 3.585A pdb=" N ILE B 708 " --> pdb=" O TRP B 704 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 721 " --> pdb=" O GLN B 717 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 755 Processing helix chain 'B' and resid 756 through 770 removed outlier: 4.109A pdb=" N LEU B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 removed outlier: 3.915A pdb=" N ILE B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 removed outlier: 4.118A pdb=" N ILE B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 removed outlier: 4.081A pdb=" N VAL B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 827 " --> pdb=" O VAL B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.631A pdb=" N VAL A 45 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU A 104 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 47 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE A 46 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY A 158 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.538A pdb=" N LEU A 202 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.974A pdb=" N VAL A 230 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342 removed outlier: 3.866A pdb=" N GLY A 337 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 482 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR A 479 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR A 499 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 481 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA7, first strand: chain 'A' and resid 569 through 571 removed outlier: 4.371A pdb=" N TRP A 570 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 579 " --> pdb=" O TRP A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.424A pdb=" N VAL B 45 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU B 104 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 47 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 46 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE B 160 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 48 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE B 183 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 159 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.145A pdb=" N VAL B 227 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS B 257 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL B 288 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER B 228 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 290 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 230 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.513A pdb=" N LYS B 341 " --> pdb=" O ASP B 480 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.642A pdb=" N PHE B 459 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 467 " --> pdb=" O PHE B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB4, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB5, first strand: chain 'B' and resid 554 through 558 removed outlier: 3.868A pdb=" N GLN B 557 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 732 through 733 removed outlier: 3.584A pdb=" N ILE B 733 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 745 " --> pdb=" O ILE B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 469 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2753 1.34 - 1.47: 3594 1.47 - 1.59: 6173 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 12658 Sorted by residual: bond pdb=" CD GLU B 80 " pdb=" OE1 GLU B 80 " ideal model delta sigma weight residual 1.249 1.364 -0.115 1.90e-02 2.77e+03 3.65e+01 bond pdb=" CG ASP B 208 " pdb=" OD2 ASP B 208 " ideal model delta sigma weight residual 1.249 1.361 -0.112 1.90e-02 2.77e+03 3.49e+01 bond pdb=" CA VAL A 802 " pdb=" CB VAL A 802 " ideal model delta sigma weight residual 1.537 1.557 -0.021 5.00e-03 4.00e+04 1.69e+01 bond pdb=" CA PRO B 729 " pdb=" C PRO B 729 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.31e+01 bond pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 1.524 1.562 -0.037 1.05e-02 9.07e+03 1.26e+01 ... (remaining 12653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 12597 2.18 - 4.36: 3778 4.36 - 6.54: 723 6.54 - 8.72: 66 8.72 - 10.91: 7 Bond angle restraints: 17171 Sorted by residual: angle pdb=" N VAL B 309 " pdb=" CA VAL B 309 " pdb=" C VAL B 309 " ideal model delta sigma weight residual 110.42 117.61 -7.19 9.60e-01 1.09e+00 5.60e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" C VAL A 308 " pdb=" N VAL A 309 " pdb=" CA VAL A 309 " ideal model delta sigma weight residual 120.56 128.80 -8.24 1.26e+00 6.30e-01 4.28e+01 angle pdb=" CA ASP B 318 " pdb=" CB ASP B 318 " pdb=" CG ASP B 318 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" CA ASN B 387 " pdb=" CB ASN B 387 " pdb=" CG ASN B 387 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 6783 17.20 - 34.40: 644 34.40 - 51.60: 147 51.60 - 68.79: 41 68.79 - 85.99: 17 Dihedral angle restraints: 7632 sinusoidal: 3053 harmonic: 4579 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 544 " pdb=" CB CYS A 544 " ideal model delta sinusoidal sigma weight residual 93.00 167.38 -74.38 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CA SER A 589 " pdb=" C SER A 589 " pdb=" N ASN A 590 " pdb=" CA ASN A 590 " ideal model delta harmonic sigma weight residual 180.00 142.29 37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA THR A 499 " pdb=" C THR A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta harmonic sigma weight residual 180.00 145.81 34.19 0 5.00e+00 4.00e-02 4.68e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1246 0.104 - 0.208: 533 0.208 - 0.312: 144 0.312 - 0.415: 26 0.415 - 0.519: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CB THR B 607 " pdb=" CA THR B 607 " pdb=" OG1 THR B 607 " pdb=" CG2 THR B 607 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CA GLU A 72 " pdb=" N GLU A 72 " pdb=" C GLU A 72 " pdb=" CB GLU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB THR B 611 " pdb=" CA THR B 611 " pdb=" OG1 THR B 611 " pdb=" CG2 THR B 611 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 1951 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 353 " 0.188 2.00e-02 2.50e+03 1.04e-01 2.17e+02 pdb=" CG TYR A 353 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 353 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR A 353 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR A 353 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 353 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 353 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 353 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 672 " 0.158 2.00e-02 2.50e+03 8.39e-02 1.41e+02 pdb=" CG TYR A 672 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 672 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR A 672 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR A 672 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR A 672 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 672 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 672 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 770 " 0.113 2.00e-02 2.50e+03 5.91e-02 6.98e+01 pdb=" CG TYR A 770 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 770 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 770 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 770 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 770 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 770 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 770 " 0.065 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 2 2.52 - 3.12: 7579 3.12 - 3.71: 19449 3.71 - 4.31: 25982 4.31 - 4.90: 42319 Nonbonded interactions: 95331 Sorted by model distance: nonbonded pdb=" O LEU B 281 " pdb=" CG ARG B 285 " model vdw 1.930 3.440 nonbonded pdb=" O LEU B 281 " pdb=" CD ARG B 285 " model vdw 2.083 3.440 nonbonded pdb=" O ARG B 521 " pdb=" N VAL B 523 " model vdw 2.569 3.120 nonbonded pdb=" OG SER B 517 " pdb=" N GLY B 518 " model vdw 2.570 3.120 nonbonded pdb=" N TRP A 570 " pdb=" O TRP A 570 " model vdw 2.587 2.496 ... (remaining 95326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 225 or (resid 226 and (name N or name CA or nam \ e C or name O or name CB )) or resid 227 through 839)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 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 : 0.015 0.115 12675 Z= 0.899 Angle : 2.083 10.905 17205 Z= 1.400 Chirality : 0.121 0.519 1954 Planarity : 0.013 0.104 2163 Dihedral : 15.162 85.992 4637 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.21 % Favored : 89.90 % Rotamer: Outliers : 3.87 % Allowed : 8.18 % Favored : 87.95 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.17), residues: 1564 helix: -2.39 (0.16), residues: 662 sheet: -2.84 (0.45), residues: 99 loop : -3.28 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 285 TYR 0.188 0.021 TYR A 353 PHE 0.097 0.022 PHE B 350 TRP 0.082 0.017 TRP B 320 HIS 0.022 0.004 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.01512 (12658) covalent geometry : angle 2.08284 (17171) SS BOND : bond 0.00940 ( 17) SS BOND : angle 2.02619 ( 34) hydrogen bonds : bond 0.22300 ( 469) hydrogen bonds : angle 8.83360 ( 1371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.6008 (OUTLIER) cc_final: 0.5343 (p-80) REVERT: A 420 MET cc_start: 0.6674 (tpt) cc_final: 0.6360 (tpp) REVERT: A 427 MET cc_start: 0.6340 (ttm) cc_final: 0.5973 (ttm) REVERT: A 727 MET cc_start: 0.6833 (tpt) cc_final: 0.6149 (ppp) REVERT: B 291 CYS cc_start: 0.7752 (m) cc_final: 0.7271 (m) REVERT: B 318 ASP cc_start: 0.5207 (t0) cc_final: 0.4898 (t0) outliers start: 53 outliers final: 13 residues processed: 216 average time/residue: 0.1169 time to fit residues: 36.5524 Evaluate side-chains 117 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 657 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 118 GLN A 173 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS A 250 GLN A 387 ASN A 506 ASN A 553 ASN A 776 ASN B 172 GLN B 173 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 506 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.142123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.106395 restraints weight = 31731.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.105168 restraints weight = 22740.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.106532 restraints weight = 19905.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.106491 restraints weight = 16015.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.106751 restraints weight = 15488.214| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12675 Z= 0.226 Angle : 0.866 9.814 17205 Z= 0.450 Chirality : 0.050 0.201 1954 Planarity : 0.006 0.055 2163 Dihedral : 7.628 58.944 1737 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 4.75 % Allowed : 12.42 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.19), residues: 1564 helix: -1.08 (0.18), residues: 680 sheet: -2.93 (0.37), residues: 124 loop : -2.82 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 521 TYR 0.024 0.002 TYR A 185 PHE 0.036 0.002 PHE B 639 TRP 0.022 0.002 TRP A 500 HIS 0.008 0.002 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00515 (12658) covalent geometry : angle 0.86346 (17171) SS BOND : bond 0.00542 ( 17) SS BOND : angle 1.79181 ( 34) hydrogen bonds : bond 0.05578 ( 469) hydrogen bonds : angle 5.57439 ( 1371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 108 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.6887 (t0) cc_final: 0.6602 (t0) REVERT: A 153 LYS cc_start: 0.8530 (mttt) cc_final: 0.8254 (mtpt) REVERT: A 303 MET cc_start: 0.7255 (mtp) cc_final: 0.6769 (mtp) REVERT: A 340 ILE cc_start: 0.8698 (pt) cc_final: 0.8428 (mt) REVERT: A 414 ILE cc_start: 0.6786 (mm) cc_final: 0.6265 (mm) REVERT: A 452 ASP cc_start: 0.7415 (m-30) cc_final: 0.6937 (t70) REVERT: B 291 CYS cc_start: 0.7355 (m) cc_final: 0.7013 (m) REVERT: B 410 MET cc_start: 0.7790 (tpp) cc_final: 0.7375 (mmm) REVERT: B 639 PHE cc_start: 0.7963 (m-80) cc_final: 0.7329 (m-80) REVERT: B 731 MET cc_start: 0.6851 (mmm) cc_final: 0.6280 (mpp) REVERT: B 827 LEU cc_start: 0.8420 (tp) cc_final: 0.7922 (mt) REVERT: B 830 MET cc_start: 0.7550 (mmm) cc_final: 0.6917 (mmm) outliers start: 65 outliers final: 37 residues processed: 162 average time/residue: 0.0907 time to fit residues: 23.2575 Evaluate side-chains 125 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 142 optimal weight: 40.0000 chunk 5 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 782 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.105879 restraints weight = 32389.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.103693 restraints weight = 30834.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.105018 restraints weight = 27113.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.105555 restraints weight = 19057.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.105789 restraints weight = 18166.176| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12675 Z= 0.288 Angle : 0.891 11.757 17205 Z= 0.463 Chirality : 0.050 0.210 1954 Planarity : 0.006 0.054 2163 Dihedral : 7.598 55.871 1730 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.83 % Favored : 88.11 % Rotamer: Outliers : 5.62 % Allowed : 14.54 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1564 helix: -0.88 (0.19), residues: 667 sheet: -2.25 (0.41), residues: 116 loop : -2.76 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 213 TYR 0.035 0.002 TYR A 185 PHE 0.037 0.003 PHE A 789 TRP 0.039 0.002 TRP A 570 HIS 0.009 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00662 (12658) covalent geometry : angle 0.88708 (17171) SS BOND : bond 0.00467 ( 17) SS BOND : angle 2.07299 ( 34) hydrogen bonds : bond 0.05517 ( 469) hydrogen bonds : angle 5.55230 ( 1371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 93 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.6368 (mtp) cc_final: 0.5908 (mtp) REVERT: A 335 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6405 (m-40) REVERT: A 403 ASN cc_start: 0.8851 (t0) cc_final: 0.8644 (t0) REVERT: A 420 MET cc_start: 0.7572 (tpp) cc_final: 0.7248 (tpp) REVERT: B 291 CYS cc_start: 0.8156 (m) cc_final: 0.7891 (m) REVERT: B 403 ASN cc_start: 0.8314 (t0) cc_final: 0.8026 (t0) REVERT: B 410 MET cc_start: 0.8334 (tpp) cc_final: 0.8012 (mmm) REVERT: B 639 PHE cc_start: 0.7527 (m-80) cc_final: 0.7183 (m-80) REVERT: B 731 MET cc_start: 0.5834 (mmm) cc_final: 0.5375 (mpp) REVERT: B 827 LEU cc_start: 0.8015 (tp) cc_final: 0.7554 (mt) REVERT: B 830 MET cc_start: 0.6461 (mmm) cc_final: 0.6082 (mmm) outliers start: 77 outliers final: 54 residues processed: 160 average time/residue: 0.0993 time to fit residues: 24.5706 Evaluate side-chains 131 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 76 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 22 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 3 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 149 optimal weight: 50.0000 chunk 128 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.140013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.103223 restraints weight = 31712.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.101903 restraints weight = 21276.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.103112 restraints weight = 18249.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.103317 restraints weight = 13787.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.103482 restraints weight = 14076.632| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12675 Z= 0.161 Angle : 0.739 8.092 17205 Z= 0.379 Chirality : 0.045 0.240 1954 Planarity : 0.005 0.056 2163 Dihedral : 6.733 51.863 1727 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 4.67 % Allowed : 16.95 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.20), residues: 1564 helix: -0.53 (0.19), residues: 681 sheet: -2.12 (0.41), residues: 118 loop : -2.62 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 203 TYR 0.022 0.002 TYR B 236 PHE 0.029 0.002 PHE A 599 TRP 0.024 0.001 TRP A 570 HIS 0.006 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00363 (12658) covalent geometry : angle 0.73590 (17171) SS BOND : bond 0.00275 ( 17) SS BOND : angle 1.73264 ( 34) hydrogen bonds : bond 0.04278 ( 469) hydrogen bonds : angle 5.15460 ( 1371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 94 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7039 (OUTLIER) cc_final: 0.6382 (p) REVERT: A 82 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7552 (ttp) REVERT: A 170 GLN cc_start: 0.8181 (mp10) cc_final: 0.7905 (mp10) REVERT: A 290 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 303 MET cc_start: 0.6574 (mtp) cc_final: 0.6042 (mtp) REVERT: A 500 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.7690 (t-100) REVERT: B 241 MET cc_start: 0.6512 (tpp) cc_final: 0.6068 (tpp) REVERT: B 410 MET cc_start: 0.8249 (tpp) cc_final: 0.8003 (mmm) REVERT: B 514 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4578 (pmm) REVERT: B 632 TYR cc_start: 0.8843 (t80) cc_final: 0.8548 (m-10) REVERT: B 639 PHE cc_start: 0.7955 (m-80) cc_final: 0.7531 (m-80) REVERT: B 718 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7050 (pp) REVERT: B 731 MET cc_start: 0.6662 (mmm) cc_final: 0.6030 (mpp) REVERT: B 827 LEU cc_start: 0.8350 (tp) cc_final: 0.7784 (mt) REVERT: B 830 MET cc_start: 0.6989 (mmm) cc_final: 0.6345 (mmm) outliers start: 64 outliers final: 39 residues processed: 147 average time/residue: 0.0874 time to fit residues: 20.4722 Evaluate side-chains 130 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 130 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 257 HIS ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.134342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.097447 restraints weight = 32455.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095851 restraints weight = 24158.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096473 restraints weight = 20830.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.096768 restraints weight = 16905.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.096907 restraints weight = 15800.437| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12675 Z= 0.302 Angle : 0.870 11.318 17205 Z= 0.449 Chirality : 0.049 0.201 1954 Planarity : 0.006 0.053 2163 Dihedral : 7.204 53.956 1724 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.83 % Favored : 88.11 % Rotamer: Outliers : 5.92 % Allowed : 17.82 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.20), residues: 1564 helix: -0.65 (0.19), residues: 685 sheet: -2.14 (0.42), residues: 117 loop : -2.80 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.030 0.002 TYR A 185 PHE 0.020 0.003 PHE A 599 TRP 0.027 0.002 TRP A 224 HIS 0.006 0.002 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00693 (12658) covalent geometry : angle 0.86688 (17171) SS BOND : bond 0.00488 ( 17) SS BOND : angle 1.96478 ( 34) hydrogen bonds : bond 0.05103 ( 469) hydrogen bonds : angle 5.47370 ( 1371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 87 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7772 (ttm) REVERT: A 170 GLN cc_start: 0.8377 (mp10) cc_final: 0.8082 (mm-40) REVERT: A 290 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7048 (m-80) REVERT: A 303 MET cc_start: 0.6801 (mtp) cc_final: 0.6092 (mtm) REVERT: A 417 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7707 (tt) REVERT: A 614 PHE cc_start: 0.7394 (t80) cc_final: 0.7103 (t80) REVERT: A 760 ASN cc_start: 0.7384 (m-40) cc_final: 0.7048 (m-40) REVERT: A 830 MET cc_start: 0.6784 (tpp) cc_final: 0.6107 (mmm) REVERT: B 367 TRP cc_start: 0.7014 (OUTLIER) cc_final: 0.3894 (m100) REVERT: B 410 MET cc_start: 0.8075 (tpp) cc_final: 0.7811 (mmm) REVERT: B 614 PHE cc_start: 0.6941 (t80) cc_final: 0.6532 (t80) REVERT: B 632 TYR cc_start: 0.8931 (t80) cc_final: 0.8571 (m-10) REVERT: B 639 PHE cc_start: 0.7979 (m-80) cc_final: 0.7517 (m-80) REVERT: B 731 MET cc_start: 0.7036 (mmm) cc_final: 0.6398 (mpp) REVERT: B 827 LEU cc_start: 0.8325 (tp) cc_final: 0.7762 (mt) REVERT: B 830 MET cc_start: 0.6818 (mmm) cc_final: 0.6154 (mmm) outliers start: 81 outliers final: 52 residues processed: 156 average time/residue: 0.0866 time to fit residues: 21.8866 Evaluate side-chains 132 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 686 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 40.0000 chunk 134 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 362 ASN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.135915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.100028 restraints weight = 32220.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097851 restraints weight = 27290.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.098822 restraints weight = 20868.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.099297 restraints weight = 17740.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099433 restraints weight = 16482.732| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12675 Z= 0.226 Angle : 0.801 10.599 17205 Z= 0.408 Chirality : 0.047 0.230 1954 Planarity : 0.005 0.050 2163 Dihedral : 6.900 52.787 1724 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.74 % Favored : 89.19 % Rotamer: Outliers : 5.62 % Allowed : 18.19 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.20), residues: 1564 helix: -0.52 (0.19), residues: 686 sheet: -2.04 (0.42), residues: 125 loop : -2.74 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 203 TYR 0.021 0.002 TYR B 185 PHE 0.042 0.002 PHE A 599 TRP 0.015 0.002 TRP B 500 HIS 0.007 0.002 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00521 (12658) covalent geometry : angle 0.79725 (17171) SS BOND : bond 0.00361 ( 17) SS BOND : angle 1.96453 ( 34) hydrogen bonds : bond 0.04562 ( 469) hydrogen bonds : angle 5.28213 ( 1371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 84 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8048 (ttp) cc_final: 0.7800 (ttm) REVERT: A 170 GLN cc_start: 0.8114 (mp10) cc_final: 0.7819 (mp10) REVERT: A 251 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: A 290 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 303 MET cc_start: 0.6889 (mtp) cc_final: 0.6252 (mtm) REVERT: A 417 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7717 (tt) REVERT: A 583 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8409 (m) REVERT: A 614 PHE cc_start: 0.7301 (t80) cc_final: 0.6998 (t80) REVERT: A 760 ASN cc_start: 0.7435 (m-40) cc_final: 0.7143 (m110) REVERT: A 830 MET cc_start: 0.6608 (tpp) cc_final: 0.6078 (mmm) REVERT: B 367 TRP cc_start: 0.7137 (OUTLIER) cc_final: 0.3862 (m100) REVERT: B 410 MET cc_start: 0.8055 (tpp) cc_final: 0.7784 (mmm) REVERT: B 614 PHE cc_start: 0.6760 (t80) cc_final: 0.6448 (t80) REVERT: B 632 TYR cc_start: 0.8921 (t80) cc_final: 0.8565 (m-10) REVERT: B 639 PHE cc_start: 0.7917 (m-80) cc_final: 0.7605 (m-80) REVERT: B 731 MET cc_start: 0.7441 (mmm) cc_final: 0.6983 (mpp) REVERT: B 827 LEU cc_start: 0.8375 (tp) cc_final: 0.7891 (mt) REVERT: B 830 MET cc_start: 0.7002 (mmm) cc_final: 0.6364 (mmm) outliers start: 77 outliers final: 51 residues processed: 152 average time/residue: 0.0827 time to fit residues: 20.4693 Evaluate side-chains 133 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 77 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 446 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 chunk 36 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 141 optimal weight: 40.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 365 ASN A 422 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.141047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.110792 restraints weight = 31592.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.108337 restraints weight = 26135.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.110103 restraints weight = 21454.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.110529 restraints weight = 15057.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.110856 restraints weight = 14379.020| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12675 Z= 0.128 Angle : 0.720 11.066 17205 Z= 0.363 Chirality : 0.044 0.182 1954 Planarity : 0.004 0.049 2163 Dihedral : 6.084 51.690 1723 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.31 % Favored : 91.62 % Rotamer: Outliers : 3.43 % Allowed : 20.96 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.20), residues: 1564 helix: -0.19 (0.19), residues: 687 sheet: -2.04 (0.44), residues: 129 loop : -2.43 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 203 TYR 0.024 0.001 TYR B 236 PHE 0.042 0.001 PHE A 599 TRP 0.016 0.001 TRP A 570 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00281 (12658) covalent geometry : angle 0.71665 (17171) SS BOND : bond 0.00375 ( 17) SS BOND : angle 1.62037 ( 34) hydrogen bonds : bond 0.03879 ( 469) hydrogen bonds : angle 5.01883 ( 1371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7785 (ttp) cc_final: 0.7476 (ttm) REVERT: A 290 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 303 MET cc_start: 0.6604 (mtp) cc_final: 0.6182 (mtp) REVERT: A 318 ASP cc_start: 0.6890 (t0) cc_final: 0.6617 (t0) REVERT: A 500 TRP cc_start: 0.8695 (OUTLIER) cc_final: 0.7725 (t-100) REVERT: A 514 MET cc_start: 0.3692 (ppp) cc_final: 0.3344 (tmm) REVERT: A 614 PHE cc_start: 0.7009 (t80) cc_final: 0.6769 (t80) REVERT: A 731 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6200 (mmp) REVERT: A 760 ASN cc_start: 0.7483 (m-40) cc_final: 0.7207 (m-40) REVERT: A 830 MET cc_start: 0.6569 (tpp) cc_final: 0.6199 (mmm) REVERT: B 367 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.3579 (m100) REVERT: B 410 MET cc_start: 0.8118 (tpp) cc_final: 0.7878 (mmm) REVERT: B 469 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: B 482 MET cc_start: 0.7572 (mmm) cc_final: 0.6595 (mtt) REVERT: B 632 TYR cc_start: 0.8759 (t80) cc_final: 0.8552 (m-10) REVERT: B 639 PHE cc_start: 0.7698 (m-80) cc_final: 0.7334 (m-80) REVERT: B 718 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6919 (pp) REVERT: B 731 MET cc_start: 0.7169 (mmm) cc_final: 0.6908 (mpp) REVERT: B 827 LEU cc_start: 0.8340 (tp) cc_final: 0.8139 (mm) REVERT: B 830 MET cc_start: 0.6447 (mmm) cc_final: 0.5988 (mmm) outliers start: 47 outliers final: 27 residues processed: 133 average time/residue: 0.0952 time to fit residues: 19.9354 Evaluate side-chains 113 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 832 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 126 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.109705 restraints weight = 30410.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.108451 restraints weight = 23775.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.109653 restraints weight = 20519.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.110043 restraints weight = 14218.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.111926 restraints weight = 13257.415| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12675 Z= 0.135 Angle : 0.714 12.749 17205 Z= 0.356 Chirality : 0.043 0.188 1954 Planarity : 0.004 0.048 2163 Dihedral : 5.963 52.227 1723 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 3.51 % Allowed : 21.40 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1564 helix: -0.10 (0.20), residues: 688 sheet: -1.79 (0.44), residues: 137 loop : -2.34 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.022 0.001 TYR B 236 PHE 0.038 0.002 PHE A 599 TRP 0.012 0.001 TRP B 500 HIS 0.007 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00301 (12658) covalent geometry : angle 0.71137 (17171) SS BOND : bond 0.00268 ( 17) SS BOND : angle 1.43896 ( 34) hydrogen bonds : bond 0.03882 ( 469) hydrogen bonds : angle 4.93036 ( 1371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7783 (ttp) cc_final: 0.7487 (ttm) REVERT: A 251 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: A 290 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: A 318 ASP cc_start: 0.7027 (t0) cc_final: 0.6695 (t0) REVERT: A 422 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.5959 (t-90) REVERT: A 482 MET cc_start: 0.8038 (mpp) cc_final: 0.7740 (mpp) REVERT: A 514 MET cc_start: 0.3760 (ppp) cc_final: 0.3327 (tmm) REVERT: A 614 PHE cc_start: 0.6917 (t80) cc_final: 0.6687 (t80) REVERT: A 731 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6196 (mmm) REVERT: A 760 ASN cc_start: 0.7423 (m-40) cc_final: 0.7128 (m-40) REVERT: A 830 MET cc_start: 0.6236 (tpp) cc_final: 0.5981 (mmm) REVERT: B 367 TRP cc_start: 0.6678 (OUTLIER) cc_final: 0.3705 (m100) REVERT: B 410 MET cc_start: 0.8090 (tpp) cc_final: 0.7820 (mmm) REVERT: B 469 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 614 PHE cc_start: 0.6142 (t80) cc_final: 0.5769 (t80) REVERT: B 639 PHE cc_start: 0.7702 (m-80) cc_final: 0.7383 (m-80) REVERT: B 640 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7366 (mm) REVERT: B 718 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6891 (pp) REVERT: B 830 MET cc_start: 0.6520 (mmm) cc_final: 0.6035 (mmm) outliers start: 48 outliers final: 33 residues processed: 122 average time/residue: 0.0894 time to fit residues: 17.5143 Evaluate side-chains 119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 832 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 149 optimal weight: 40.0000 chunk 82 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.101754 restraints weight = 29455.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.100928 restraints weight = 20865.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.103213 restraints weight = 17530.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.103067 restraints weight = 13039.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.103093 restraints weight = 13352.488| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12675 Z= 0.138 Angle : 0.728 13.620 17205 Z= 0.358 Chirality : 0.043 0.216 1954 Planarity : 0.004 0.056 2163 Dihedral : 5.894 52.690 1723 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 3.21 % Allowed : 21.91 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.20), residues: 1564 helix: -0.08 (0.19), residues: 690 sheet: -2.05 (0.42), residues: 137 loop : -2.26 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.022 0.002 TYR B 236 PHE 0.038 0.002 PHE A 599 TRP 0.012 0.001 TRP B 500 HIS 0.007 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00311 (12658) covalent geometry : angle 0.72569 (17171) SS BOND : bond 0.00273 ( 17) SS BOND : angle 1.58858 ( 34) hydrogen bonds : bond 0.03880 ( 469) hydrogen bonds : angle 4.91586 ( 1371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 79 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7828 (ttp) cc_final: 0.7560 (ttm) REVERT: A 251 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: A 290 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: A 303 MET cc_start: 0.6538 (mtp) cc_final: 0.6184 (mtp) REVERT: A 318 ASP cc_start: 0.7026 (t0) cc_final: 0.6678 (t0) REVERT: A 482 MET cc_start: 0.8070 (mpp) cc_final: 0.7752 (mpp) REVERT: A 514 MET cc_start: 0.3507 (ppp) cc_final: 0.3196 (tmm) REVERT: A 614 PHE cc_start: 0.7340 (t80) cc_final: 0.7048 (t80) REVERT: A 731 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: A 760 ASN cc_start: 0.7367 (m-40) cc_final: 0.7145 (m-40) REVERT: A 830 MET cc_start: 0.7301 (tpp) cc_final: 0.6387 (mmm) REVERT: B 367 TRP cc_start: 0.6720 (OUTLIER) cc_final: 0.3738 (m100) REVERT: B 410 MET cc_start: 0.8201 (tpp) cc_final: 0.7948 (mmm) REVERT: B 469 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: B 639 PHE cc_start: 0.7969 (m-80) cc_final: 0.7625 (m-80) REVERT: B 718 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6916 (pp) REVERT: B 830 MET cc_start: 0.7321 (mmm) cc_final: 0.6485 (mmm) REVERT: B 835 MET cc_start: 0.7143 (tmm) cc_final: 0.6115 (tmm) outliers start: 44 outliers final: 35 residues processed: 118 average time/residue: 0.0863 time to fit residues: 16.3054 Evaluate side-chains 118 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 832 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 106 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.144219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.111987 restraints weight = 30670.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.111113 restraints weight = 29573.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.112468 restraints weight = 21195.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.113130 restraints weight = 16787.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.113319 restraints weight = 15108.085| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12675 Z= 0.127 Angle : 0.737 15.490 17205 Z= 0.359 Chirality : 0.043 0.190 1954 Planarity : 0.004 0.052 2163 Dihedral : 5.725 52.519 1723 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 2.99 % Allowed : 22.50 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1564 helix: -0.02 (0.19), residues: 697 sheet: -1.91 (0.43), residues: 137 loop : -2.20 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.023 0.001 TYR A 759 PHE 0.037 0.001 PHE A 599 TRP 0.012 0.001 TRP A 570 HIS 0.006 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00284 (12658) covalent geometry : angle 0.73450 (17171) SS BOND : bond 0.00257 ( 17) SS BOND : angle 1.46762 ( 34) hydrogen bonds : bond 0.03718 ( 469) hydrogen bonds : angle 4.85276 ( 1371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7754 (ttp) cc_final: 0.7436 (ttp) REVERT: A 170 GLN cc_start: 0.7767 (mp10) cc_final: 0.7124 (tt0) REVERT: A 251 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: A 290 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: A 303 MET cc_start: 0.6241 (mtp) cc_final: 0.5955 (mtp) REVERT: A 318 ASP cc_start: 0.6887 (t0) cc_final: 0.6538 (t0) REVERT: A 482 MET cc_start: 0.8386 (mpp) cc_final: 0.8176 (mpp) REVERT: A 514 MET cc_start: 0.3543 (ppp) cc_final: 0.3253 (tmm) REVERT: A 614 PHE cc_start: 0.7117 (t80) cc_final: 0.6894 (t80) REVERT: A 760 ASN cc_start: 0.7218 (m-40) cc_final: 0.6941 (m110) REVERT: B 367 TRP cc_start: 0.6493 (OUTLIER) cc_final: 0.3560 (m100) REVERT: B 410 MET cc_start: 0.8037 (tpp) cc_final: 0.7831 (mmm) REVERT: B 469 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 639 PHE cc_start: 0.7622 (m-80) cc_final: 0.7354 (m-80) REVERT: B 718 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6887 (pp) REVERT: B 830 MET cc_start: 0.6237 (mmm) cc_final: 0.5888 (mmm) REVERT: B 835 MET cc_start: 0.6705 (tmm) cc_final: 0.5519 (tmm) outliers start: 41 outliers final: 33 residues processed: 116 average time/residue: 0.0952 time to fit residues: 17.5303 Evaluate side-chains 119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 832 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 10.0000 chunk 140 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.139150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.109067 restraints weight = 31108.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.105971 restraints weight = 27613.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.107201 restraints weight = 24410.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.108462 restraints weight = 17917.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.108507 restraints weight = 15395.205| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12675 Z= 0.226 Angle : 0.812 15.229 17205 Z= 0.405 Chirality : 0.046 0.181 1954 Planarity : 0.005 0.053 2163 Dihedral : 6.261 54.727 1723 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.46 % Favored : 90.47 % Rotamer: Outliers : 2.99 % Allowed : 22.72 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1564 helix: -0.11 (0.20), residues: 691 sheet: -1.77 (0.43), residues: 137 loop : -2.43 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 221 TYR 0.027 0.002 TYR A 185 PHE 0.040 0.002 PHE A 789 TRP 0.012 0.002 TRP A 500 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00522 (12658) covalent geometry : angle 0.81006 (17171) SS BOND : bond 0.00362 ( 17) SS BOND : angle 1.59234 ( 34) hydrogen bonds : bond 0.04338 ( 469) hydrogen bonds : angle 5.06681 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.70 seconds wall clock time: 40 minutes 36.38 seconds (2436.38 seconds total)