Starting phenix.real_space_refine on Wed Jul 30 13:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_30671_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_30671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_30671.map" model { file = "/net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_30671_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dgd_30671/07_2025/7dgd_30671_neut.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.89, per 1000 atoms: 0.64 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: 2.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.34 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: 3.89 Time building geometry restraints manager: 3.37 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (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 TRP 0.082 0.017 TRP B 320 HIS 0.022 0.004 HIS B 383 PHE 0.097 0.022 PHE B 350 TYR 0.188 0.021 TYR A 353 ARG 0.006 0.001 ARG B 285 Details of bonding type rmsd hydrogen bonds : bond 0.22300 ( 469) hydrogen bonds : angle 8.83360 ( 1371) SS BOND : bond 0.00940 ( 17) SS BOND : angle 2.02619 ( 34) covalent geometry : bond 0.01512 (12658) covalent geometry : angle 2.08284 (17171) *********************** 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 : 1.347 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: 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: 0.6359 (tpp) REVERT: A 427 MET cc_start: 0.6341 (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: 0.2487 time to fit residues: 77.8338 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 : 1.394 ------------------------------------------------------------------------------- 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 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 173 ASN A 182 GLN A 231 HIS A 250 GLN A 365 ASN A 387 ASN A 485 GLN A 506 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 173 ASN B 182 GLN 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 ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.144520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.108524 restraints weight = 31392.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.106979 restraints weight = 21677.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.108164 restraints weight = 18751.052| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12675 Z= 0.181 Angle : 0.814 10.044 17205 Z= 0.420 Chirality : 0.048 0.206 1954 Planarity : 0.005 0.061 2163 Dihedral : 7.424 59.593 1737 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.94 % Rotamer: Outliers : 4.60 % Allowed : 11.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.19), residues: 1564 helix: -0.94 (0.18), residues: 680 sheet: -2.85 (0.38), residues: 124 loop : -2.73 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 500 HIS 0.006 0.001 HIS A 428 PHE 0.032 0.002 PHE A 599 TYR 0.022 0.002 TYR A 672 ARG 0.007 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 469) hydrogen bonds : angle 5.46925 ( 1371) SS BOND : bond 0.00380 ( 17) SS BOND : angle 1.77021 ( 34) covalent geometry : bond 0.00402 (12658) covalent geometry : angle 0.81102 (17171) *********************** 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 170 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 107 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.5028 (p-80) REVERT: A 90 ASN cc_start: 0.6819 (t0) cc_final: 0.6516 (t0) REVERT: A 303 MET cc_start: 0.7349 (mtp) cc_final: 0.6911 (mtp) REVERT: A 414 ILE cc_start: 0.6998 (mm) cc_final: 0.6530 (mm) REVERT: B 318 ASP cc_start: 0.7094 (t0) cc_final: 0.6840 (t0) REVERT: B 410 MET cc_start: 0.7231 (tpp) cc_final: 0.6967 (mmm) REVERT: B 514 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4853 (pmm) REVERT: B 614 PHE cc_start: 0.7910 (t80) cc_final: 0.7626 (t80) REVERT: B 632 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: B 639 PHE cc_start: 0.8007 (m-80) cc_final: 0.7443 (m-80) REVERT: B 731 MET cc_start: 0.6988 (mmm) cc_final: 0.6439 (mpp) REVERT: B 827 LEU cc_start: 0.8408 (tp) cc_final: 0.7925 (mt) REVERT: B 830 MET cc_start: 0.7646 (mmm) cc_final: 0.6922 (mmm) outliers start: 63 outliers final: 33 residues processed: 160 average time/residue: 0.1948 time to fit residues: 49.3661 Evaluate side-chains 127 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 281 LEU Chi-restraints excluded: chain B residue 317 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.134211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097516 restraints weight = 32703.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.095971 restraints weight = 21873.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097249 restraints weight = 18579.493| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 12675 Z= 0.373 Angle : 0.984 13.424 17205 Z= 0.511 Chirality : 0.054 0.254 1954 Planarity : 0.007 0.064 2163 Dihedral : 7.857 57.847 1729 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.28 % Favored : 87.60 % Rotamer: Outliers : 5.70 % Allowed : 14.54 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.19), residues: 1564 helix: -0.95 (0.19), residues: 677 sheet: -2.37 (0.40), residues: 114 loop : -2.93 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 570 HIS 0.009 0.002 HIS A 422 PHE 0.036 0.003 PHE A 599 TYR 0.041 0.003 TYR A 185 ARG 0.011 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.05952 ( 469) hydrogen bonds : angle 5.79846 ( 1371) SS BOND : bond 0.00618 ( 17) SS BOND : angle 2.17435 ( 34) covalent geometry : bond 0.00863 (12658) covalent geometry : angle 0.98047 (17171) *********************** 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 174 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 96 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.5010 (OUTLIER) cc_final: 0.4683 (mm) REVERT: A 153 LYS cc_start: 0.8499 (mttt) cc_final: 0.8135 (mtpt) REVERT: A 403 ASN cc_start: 0.8926 (t0) cc_final: 0.8682 (t0) REVERT: A 417 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7611 (tt) REVERT: A 420 MET cc_start: 0.7739 (tpp) cc_final: 0.7383 (tpp) REVERT: A 438 LEU cc_start: 0.7373 (mt) cc_final: 0.7159 (pt) REVERT: A 482 MET cc_start: 0.7045 (mtt) cc_final: 0.6742 (mtt) REVERT: A 614 PHE cc_start: 0.7253 (t80) cc_final: 0.7035 (t80) REVERT: B 291 CYS cc_start: 0.8185 (m) cc_final: 0.7951 (m) REVERT: B 317 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7746 (t) REVERT: B 403 ASN cc_start: 0.8388 (t0) cc_final: 0.8056 (t0) REVERT: B 410 MET cc_start: 0.8367 (tpp) cc_final: 0.8032 (mmm) REVERT: B 639 PHE cc_start: 0.7853 (m-80) cc_final: 0.7478 (m-80) REVERT: B 731 MET cc_start: 0.6734 (mmm) cc_final: 0.6054 (mpp) REVERT: B 827 LEU cc_start: 0.8288 (tp) cc_final: 0.7788 (mt) REVERT: B 830 MET cc_start: 0.7060 (mmm) cc_final: 0.6503 (mmm) outliers start: 78 outliers final: 48 residues processed: 162 average time/residue: 0.2300 time to fit residues: 56.9153 Evaluate side-chains 127 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 76 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE 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 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 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 436 VAL 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 38 VAL 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 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 303 MET Chi-restraints excluded: chain B residue 317 SER 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 632 TYR Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 798 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 660 GLN ** B 182 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** 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 = 0.4565 r_free = 0.4565 target = 0.140000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.102950 restraints weight = 31906.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.102276 restraints weight = 20171.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.104047 restraints weight = 16213.482| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12675 Z= 0.158 Angle : 0.748 10.261 17205 Z= 0.381 Chirality : 0.045 0.206 1954 Planarity : 0.005 0.054 2163 Dihedral : 6.774 52.878 1726 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 4.46 % Allowed : 17.09 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.19), residues: 1564 helix: -0.59 (0.19), residues: 681 sheet: -2.18 (0.39), residues: 123 loop : -2.69 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 570 HIS 0.007 0.001 HIS A 422 PHE 0.029 0.002 PHE A 599 TYR 0.020 0.002 TYR A 672 ARG 0.007 0.001 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 469) hydrogen bonds : angle 5.23716 ( 1371) SS BOND : bond 0.00346 ( 17) SS BOND : angle 1.75548 ( 34) covalent geometry : bond 0.00356 (12658) covalent geometry : angle 0.74467 (17171) *********************** 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 155 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 94 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7044 (OUTLIER) cc_final: 0.6412 (p) REVERT: A 82 MET cc_start: 0.8083 (ttp) cc_final: 0.7826 (ttp) REVERT: A 153 LYS cc_start: 0.8558 (mttt) cc_final: 0.8339 (mtpt) REVERT: A 290 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: A 303 MET cc_start: 0.6194 (mtp) cc_final: 0.5844 (mtp) REVERT: A 420 MET cc_start: 0.7662 (tpp) cc_final: 0.7429 (tpp) REVERT: A 500 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7709 (t-100) REVERT: A 731 MET cc_start: 0.7411 (mmp) cc_final: 0.7183 (mmp) REVERT: B 180 ILE cc_start: 0.8325 (mt) cc_final: 0.8108 (mt) REVERT: B 241 MET cc_start: 0.6367 (tpp) cc_final: 0.5934 (tpp) REVERT: B 410 MET cc_start: 0.8318 (tpp) cc_final: 0.7964 (mmm) REVERT: B 438 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6087 (tp) REVERT: B 514 MET cc_start: 0.5122 (OUTLIER) cc_final: 0.4577 (pmm) REVERT: B 614 PHE cc_start: 0.7105 (t80) cc_final: 0.6834 (t80) REVERT: B 632 TYR cc_start: 0.8954 (t80) cc_final: 0.8626 (m-10) REVERT: B 639 PHE cc_start: 0.7835 (m-80) cc_final: 0.7396 (m-80) REVERT: B 670 MET cc_start: 0.6110 (ppp) cc_final: 0.5903 (ppp) REVERT: B 727 MET cc_start: 0.5577 (ppp) cc_final: 0.4846 (ppp) REVERT: B 731 MET cc_start: 0.6684 (mmm) cc_final: 0.6031 (mpp) REVERT: B 827 LEU cc_start: 0.8257 (tp) cc_final: 0.7746 (mt) REVERT: B 830 MET cc_start: 0.6926 (mmm) cc_final: 0.6349 (mmm) outliers start: 61 outliers final: 36 residues processed: 145 average time/residue: 0.1937 time to fit residues: 44.0680 Evaluate side-chains 120 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 84 HIS 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 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 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 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 281 LEU 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 438 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 422 HIS ** 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 406 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 = 0.4515 r_free = 0.4515 target = 0.135903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.098816 restraints weight = 31852.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097415 restraints weight = 20838.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.098728 restraints weight = 18371.714| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12675 Z= 0.243 Angle : 0.810 10.939 17205 Z= 0.414 Chirality : 0.047 0.211 1954 Planarity : 0.005 0.052 2163 Dihedral : 6.978 53.785 1725 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.19 % Favored : 88.75 % Rotamer: Outliers : 5.55 % Allowed : 17.31 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1564 helix: -0.57 (0.19), residues: 682 sheet: -2.03 (0.42), residues: 121 loop : -2.75 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 570 HIS 0.005 0.002 HIS A 422 PHE 0.022 0.002 PHE A 599 TYR 0.027 0.002 TYR A 185 ARG 0.005 0.001 ARG B 521 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 469) hydrogen bonds : angle 5.35821 ( 1371) SS BOND : bond 0.00398 ( 17) SS BOND : angle 1.85134 ( 34) covalent geometry : bond 0.00555 (12658) covalent geometry : angle 0.80641 (17171) *********************** 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 160 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 84 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.8313 (mp10) cc_final: 0.7992 (mp10) REVERT: A 290 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 303 MET cc_start: 0.6601 (mtp) cc_final: 0.5993 (mtp) REVERT: A 417 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 420 MET cc_start: 0.7679 (tpp) cc_final: 0.7296 (tpp) REVERT: A 614 PHE cc_start: 0.7375 (t80) cc_final: 0.7130 (t80) REVERT: A 731 MET cc_start: 0.7656 (mmp) cc_final: 0.6978 (mmp) REVERT: A 830 MET cc_start: 0.6785 (tpp) cc_final: 0.6160 (mmm) REVERT: B 367 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.3674 (m100) REVERT: B 410 MET cc_start: 0.8201 (tpp) cc_final: 0.7947 (mmm) REVERT: B 632 TYR cc_start: 0.8897 (t80) cc_final: 0.8603 (m-10) REVERT: B 639 PHE cc_start: 0.7862 (m-80) cc_final: 0.7390 (m-80) REVERT: B 670 MET cc_start: 0.6035 (ppp) cc_final: 0.5735 (ppp) REVERT: B 718 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6686 (pp) REVERT: B 731 MET cc_start: 0.6865 (mmm) cc_final: 0.6231 (mpp) REVERT: B 827 LEU cc_start: 0.8217 (tp) cc_final: 0.7744 (mt) REVERT: B 830 MET cc_start: 0.6661 (mmm) cc_final: 0.6081 (mmm) outliers start: 76 outliers final: 46 residues processed: 153 average time/residue: 0.1946 time to fit residues: 47.5189 Evaluate side-chains 126 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 76 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 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 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 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 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 718 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 141 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 406 GLN ** 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 = 0.4602 r_free = 0.4602 target = 0.142150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.104328 restraints weight = 31583.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.103471 restraints weight = 19212.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.105332 restraints weight = 15308.190| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12675 Z= 0.132 Angle : 0.715 9.509 17205 Z= 0.361 Chirality : 0.044 0.184 1954 Planarity : 0.004 0.048 2163 Dihedral : 6.181 51.707 1723 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 3.58 % Allowed : 19.58 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.20), residues: 1564 helix: -0.25 (0.19), residues: 678 sheet: -1.92 (0.41), residues: 130 loop : -2.50 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 570 HIS 0.003 0.001 HIS B 231 PHE 0.020 0.001 PHE A 599 TYR 0.018 0.001 TYR A 672 ARG 0.006 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 469) hydrogen bonds : angle 5.00711 ( 1371) SS BOND : bond 0.00343 ( 17) SS BOND : angle 1.75500 ( 34) covalent geometry : bond 0.00292 (12658) covalent geometry : angle 0.71097 (17171) *********************** 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 143 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7523 (ttp) REVERT: A 170 GLN cc_start: 0.8093 (mp10) cc_final: 0.7240 (tt0) REVERT: A 290 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: A 303 MET cc_start: 0.6533 (mtp) cc_final: 0.5987 (mtp) REVERT: A 420 MET cc_start: 0.7785 (tpp) cc_final: 0.6450 (ttp) REVERT: A 500 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.7726 (t-100) REVERT: A 614 PHE cc_start: 0.7242 (t80) cc_final: 0.6962 (t80) REVERT: A 731 MET cc_start: 0.7807 (mmp) cc_final: 0.7145 (mmp) REVERT: A 830 MET cc_start: 0.7182 (tpp) cc_final: 0.6409 (mmm) REVERT: B 241 MET cc_start: 0.7121 (tpp) cc_final: 0.6714 (tpp) REVERT: B 367 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.3748 (m100) REVERT: B 410 MET cc_start: 0.8090 (tpp) cc_final: 0.7825 (mmm) REVERT: B 469 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: B 482 MET cc_start: 0.7745 (mmm) cc_final: 0.6757 (mtt) REVERT: B 614 PHE cc_start: 0.6809 (t80) cc_final: 0.6335 (t80) REVERT: B 632 TYR cc_start: 0.8905 (t80) cc_final: 0.8596 (m-10) REVERT: B 639 PHE cc_start: 0.7896 (m-80) cc_final: 0.7401 (m-80) REVERT: B 670 MET cc_start: 0.6415 (ppp) cc_final: 0.6079 (ppp) REVERT: B 731 MET cc_start: 0.7561 (mmm) cc_final: 0.7130 (mpp) REVERT: B 827 LEU cc_start: 0.8505 (tp) cc_final: 0.8279 (mm) REVERT: B 830 MET cc_start: 0.7020 (mmm) cc_final: 0.6419 (mmm) outliers start: 49 outliers final: 34 residues processed: 136 average time/residue: 0.2003 time to fit residues: 43.3069 Evaluate side-chains 119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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 290 PHE Chi-restraints excluded: chain A residue 422 HIS 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 670 MET Chi-restraints excluded: chain A residue 760 ASN 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 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 420 MET 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 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 35 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 2 optimal weight: 0.0050 chunk 64 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 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 406 GLN ** 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 = 0.4573 r_free = 0.4573 target = 0.140439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.103959 restraints weight = 31630.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.102615 restraints weight = 20187.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.104189 restraints weight = 16719.906| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.6138 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= 0.145 Angle : 0.719 11.328 17205 Z= 0.360 Chirality : 0.044 0.182 1954 Planarity : 0.004 0.046 2163 Dihedral : 6.080 52.552 1723 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.92 % Rotamer: Outliers : 3.87 % Allowed : 20.16 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1564 helix: -0.21 (0.19), residues: 691 sheet: -1.89 (0.42), residues: 133 loop : -2.42 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 570 HIS 0.019 0.001 HIS A 422 PHE 0.017 0.001 PHE A 599 TYR 0.017 0.001 TYR A 672 ARG 0.004 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 469) hydrogen bonds : angle 4.96827 ( 1371) SS BOND : bond 0.00260 ( 17) SS BOND : angle 1.65733 ( 34) covalent geometry : bond 0.00329 (12658) covalent geometry : angle 0.71621 (17171) *********************** 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 136 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7739 (mp10) cc_final: 0.7511 (mp10) REVERT: A 182 GLN cc_start: 0.5462 (OUTLIER) cc_final: 0.5027 (pt0) REVERT: A 251 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 290 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 303 MET cc_start: 0.6577 (mtp) cc_final: 0.6054 (mtp) REVERT: A 410 MET cc_start: 0.8276 (mmm) cc_final: 0.7912 (mmm) REVERT: A 417 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7567 (tt) REVERT: A 420 MET cc_start: 0.7557 (tpp) cc_final: 0.5933 (ttm) REVERT: A 422 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.5979 (t-90) REVERT: A 427 MET cc_start: 0.8033 (ttp) cc_final: 0.7244 (ttm) REVERT: A 614 PHE cc_start: 0.7052 (t80) cc_final: 0.6808 (t80) REVERT: A 731 MET cc_start: 0.7479 (mmp) cc_final: 0.6951 (mmp) REVERT: A 830 MET cc_start: 0.6945 (tpp) cc_final: 0.6365 (mmm) REVERT: B 367 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.3548 (m100) REVERT: B 410 MET cc_start: 0.8267 (tpp) cc_final: 0.8011 (mmm) REVERT: B 469 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: B 632 TYR cc_start: 0.8827 (t80) cc_final: 0.8575 (m-10) REVERT: B 639 PHE cc_start: 0.7840 (m-80) cc_final: 0.7382 (m-80) REVERT: B 670 MET cc_start: 0.6318 (ppp) cc_final: 0.5986 (ppp) REVERT: B 718 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6926 (pp) REVERT: B 731 MET cc_start: 0.7424 (mmm) cc_final: 0.7108 (mpp) REVERT: B 830 MET cc_start: 0.6742 (mmm) cc_final: 0.6176 (mmm) outliers start: 53 outliers final: 39 residues processed: 129 average time/residue: 0.2015 time to fit residues: 40.9294 Evaluate side-chains 122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS 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 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 251 GLU 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 417 ILE Chi-restraints excluded: chain A residue 422 HIS 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 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 760 ASN 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 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 344 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.0040 chunk 62 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 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 406 GLN ** 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 = 0.4533 r_free = 0.4533 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.100692 restraints weight = 31258.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.098973 restraints weight = 20812.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.100313 restraints weight = 18150.225| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12675 Z= 0.205 Angle : 0.778 14.992 17205 Z= 0.391 Chirality : 0.045 0.198 1954 Planarity : 0.005 0.048 2163 Dihedral : 6.336 53.644 1723 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.29 % Favored : 89.64 % Rotamer: Outliers : 4.89 % Allowed : 19.65 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1564 helix: -0.31 (0.19), residues: 689 sheet: -1.79 (0.44), residues: 127 loop : -2.54 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 224 HIS 0.028 0.002 HIS A 422 PHE 0.017 0.002 PHE B 201 TYR 0.022 0.002 TYR B 185 ARG 0.004 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 469) hydrogen bonds : angle 5.09635 ( 1371) SS BOND : bond 0.00463 ( 17) SS BOND : angle 1.56234 ( 34) covalent geometry : bond 0.00472 (12658) covalent geometry : angle 0.77547 (17171) *********************** 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 147 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 80 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6260 (mp) REVERT: A 182 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5369 (pt0) REVERT: A 251 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: A 303 MET cc_start: 0.6648 (mtp) cc_final: 0.6012 (mtp) REVERT: A 420 MET cc_start: 0.7515 (tpp) cc_final: 0.6217 (ttm) REVERT: A 422 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6167 (t-90) REVERT: A 442 MET cc_start: 0.6159 (ttt) cc_final: 0.5935 (ttm) REVERT: A 469 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 514 MET cc_start: 0.3674 (ppp) cc_final: 0.3222 (tmm) REVERT: A 614 PHE cc_start: 0.7228 (t80) cc_final: 0.6996 (t80) REVERT: A 731 MET cc_start: 0.7436 (mmp) cc_final: 0.6906 (mmp) REVERT: A 830 MET cc_start: 0.6911 (tpp) cc_final: 0.6368 (mmm) REVERT: B 410 MET cc_start: 0.8224 (tpp) cc_final: 0.7990 (mmm) REVERT: B 639 PHE cc_start: 0.7727 (m-80) cc_final: 0.7490 (m-80) REVERT: B 670 MET cc_start: 0.6239 (ppp) cc_final: 0.5906 (ppp) REVERT: B 718 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6943 (pp) REVERT: B 792 TYR cc_start: 0.6801 (m-10) cc_final: 0.6471 (m-80) REVERT: B 830 MET cc_start: 0.6810 (mmm) cc_final: 0.6233 (mmm) outliers start: 67 outliers final: 46 residues processed: 141 average time/residue: 0.1843 time to fit residues: 42.0189 Evaluate side-chains 126 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 74 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 159 VAL 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 207 SER Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 422 HIS 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 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain B residue 108 SER 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 189 SER 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 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 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 594 ILE Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 22 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** 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 = 0.4556 r_free = 0.4556 target = 0.139294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.109358 restraints weight = 31581.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.107643 restraints weight = 29042.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.109086 restraints weight = 23753.914| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12675 Z= 0.154 Angle : 0.740 12.138 17205 Z= 0.369 Chirality : 0.045 0.260 1954 Planarity : 0.005 0.046 2163 Dihedral : 6.074 52.983 1723 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.02 % Favored : 90.92 % Rotamer: Outliers : 3.73 % Allowed : 20.82 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1564 helix: -0.21 (0.19), residues: 686 sheet: -2.08 (0.41), residues: 138 loop : -2.35 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 500 HIS 0.022 0.001 HIS A 422 PHE 0.015 0.001 PHE A 599 TYR 0.022 0.002 TYR A 759 ARG 0.006 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 469) hydrogen bonds : angle 4.96348 ( 1371) SS BOND : bond 0.00286 ( 17) SS BOND : angle 1.65483 ( 34) covalent geometry : bond 0.00353 (12658) covalent geometry : angle 0.73720 (17171) *********************** 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 125 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 74 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLN cc_start: 0.7857 (mp10) cc_final: 0.7657 (mp10) REVERT: A 251 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: A 303 MET cc_start: 0.6531 (mtp) cc_final: 0.5923 (mtp) REVERT: A 420 MET cc_start: 0.7439 (tpp) cc_final: 0.6210 (ttt) REVERT: A 422 HIS cc_start: 0.6734 (OUTLIER) cc_final: 0.6014 (t-90) REVERT: A 442 MET cc_start: 0.6216 (ttt) cc_final: 0.5958 (ttm) REVERT: A 469 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: A 482 MET cc_start: 0.8434 (mpp) cc_final: 0.8226 (mpp) REVERT: A 500 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.7886 (t-100) REVERT: A 514 MET cc_start: 0.3298 (ppp) cc_final: 0.3034 (tmm) REVERT: A 731 MET cc_start: 0.6692 (mmp) cc_final: 0.6327 (mmp) REVERT: B 410 MET cc_start: 0.8209 (tpp) cc_final: 0.7923 (mmm) REVERT: B 469 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 639 PHE cc_start: 0.7492 (m-80) cc_final: 0.7180 (m-80) REVERT: B 718 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6897 (pp) REVERT: B 830 MET cc_start: 0.6261 (mmm) cc_final: 0.5919 (mmm) outliers start: 51 outliers final: 39 residues processed: 118 average time/residue: 0.1837 time to fit residues: 35.2093 Evaluate side-chains 115 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 70 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE 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 308 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 422 HIS 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 670 MET Chi-restraints excluded: chain A residue 701 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** B 77 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 406 GLN ** 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 = 0.4577 r_free = 0.4577 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.110652 restraints weight = 31065.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.109579 restraints weight = 26885.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.110569 restraints weight = 22501.719| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12675 Z= 0.143 Angle : 0.752 12.814 17205 Z= 0.371 Chirality : 0.044 0.201 1954 Planarity : 0.004 0.045 2163 Dihedral : 5.950 53.177 1723 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.57 % Favored : 91.37 % Rotamer: Outliers : 3.43 % Allowed : 21.40 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1564 helix: -0.24 (0.19), residues: 695 sheet: -1.96 (0.41), residues: 138 loop : -2.30 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 570 HIS 0.011 0.001 HIS A 422 PHE 0.015 0.001 PHE A 599 TYR 0.025 0.001 TYR A 759 ARG 0.005 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 469) hydrogen bonds : angle 4.93186 ( 1371) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.52850 ( 34) covalent geometry : bond 0.00321 (12658) covalent geometry : angle 0.74947 (17171) ********************** 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 123 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 76 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 303 MET cc_start: 0.6532 (mtp) cc_final: 0.5923 (mtp) REVERT: A 420 MET cc_start: 0.7352 (tpp) cc_final: 0.6272 (tpp) REVERT: A 427 MET cc_start: 0.7882 (ttp) cc_final: 0.7428 (ttm) REVERT: A 500 TRP cc_start: 0.8856 (OUTLIER) cc_final: 0.7872 (t-100) REVERT: A 514 MET cc_start: 0.3345 (ppp) cc_final: 0.3116 (tmm) REVERT: A 731 MET cc_start: 0.6656 (mmp) cc_final: 0.6212 (mmp) REVERT: B 236 TYR cc_start: 0.7111 (t80) cc_final: 0.6869 (t80) REVERT: B 410 MET cc_start: 0.8209 (tpp) cc_final: 0.7895 (mmm) REVERT: B 469 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: B 639 PHE cc_start: 0.7520 (m-80) cc_final: 0.7212 (m-80) REVERT: B 718 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6906 (pp) REVERT: B 830 MET cc_start: 0.6331 (mmm) cc_final: 0.5951 (mmm) outliers start: 47 outliers final: 38 residues processed: 116 average time/residue: 0.2059 time to fit residues: 38.3543 Evaluate side-chains 115 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 73 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE 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 308 VAL Chi-restraints excluded: chain A residue 339 THR 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 535 VAL Chi-restraints excluded: chain A residue 558 ASP 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 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 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR 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 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 572 ASN Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 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 406 GLN ** 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 = 0.4573 r_free = 0.4573 target = 0.140031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.101374 restraints weight = 31580.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.099166 restraints weight = 22236.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.101140 restraints weight = 21322.038| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.6940 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= 0.193 Angle : 0.784 13.183 17205 Z= 0.391 Chirality : 0.045 0.187 1954 Planarity : 0.005 0.045 2163 Dihedral : 6.181 54.489 1723 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.97 % Favored : 89.96 % Rotamer: Outliers : 3.65 % Allowed : 21.18 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1564 helix: -0.25 (0.19), residues: 692 sheet: -2.07 (0.41), residues: 140 loop : -2.39 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 224 HIS 0.004 0.001 HIS A 231 PHE 0.037 0.002 PHE A 831 TYR 0.025 0.002 TYR A 759 ARG 0.005 0.001 ARG B 278 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 469) hydrogen bonds : angle 5.04610 ( 1371) SS BOND : bond 0.00327 ( 17) SS BOND : angle 1.55739 ( 34) covalent geometry : bond 0.00445 (12658) covalent geometry : angle 0.78186 (17171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4388.22 seconds wall clock time: 77 minutes 45.24 seconds (4665.24 seconds total)