Starting phenix.real_space_refine on Mon May 4 15:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lpz_63281/05_2026/9lpz_63281.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 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 88 5.16 5 C 13852 2.51 5 N 3701 2.21 5 O 4042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21683 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain: "D" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain: "B" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6675 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 803} Chain breaks: 1 Chain: "C" Number of atoms: 6668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6668 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 802} Chain breaks: 1 Time building chain proxies: 4.83, per 1000 atoms: 0.22 Number of scatterers: 21683 At special positions: 0 Unit cell: (140.28, 147.84, 133.56, 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 88 16.00 O 4042 8.00 N 3701 7.00 C 13852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 396 " distance=2.89 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: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 14 sheets defined 56.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.587A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 193 through 215 Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.578A pdb=" N THR A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 249 removed outlier: 4.559A pdb=" N GLY A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 276 through 305 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 419 through 431 removed outlier: 4.022A pdb=" N PHE A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.540A pdb=" N VAL A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.618A pdb=" N HIS A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.722A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 514 removed outlier: 3.707A pdb=" N THR A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.945A pdb=" N THR A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.651A pdb=" N ARG A 553 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 591 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 117 through 131 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 175 removed outlier: 3.503A pdb=" N LEU D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 214 Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 217 through 227 removed outlier: 3.675A pdb=" N LYS D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.762A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 276 through 304 removed outlier: 3.893A pdb=" N ILE D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.629A pdb=" N PHE D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 370 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 419 through 430 removed outlier: 4.176A pdb=" N PHE D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 455 removed outlier: 3.560A pdb=" N VAL D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.636A pdb=" N HIS D 479 " --> pdb=" O PRO D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.773A pdb=" N THR D 501 " --> pdb=" O GLY D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 515 through 518 removed outlier: 4.142A pdb=" N ASN D 518 " --> pdb=" O PRO D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 518' Processing helix chain 'D' and resid 521 through 532 removed outlier: 3.590A pdb=" N ILE D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 577 through 591 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 101 through 132 Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.513A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 341 through 372 removed outlier: 3.572A pdb=" N GLY B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 Proline residue: B 381 - end of helix Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.562A pdb=" N LEU B 435 " --> pdb=" O PRO B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 447 through 470 Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.622A pdb=" N LEU B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 580 through 588 Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 654 through 665 removed outlier: 3.513A pdb=" N LYS B 657 " --> pdb=" O ASN B 654 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 665 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 694 Processing helix chain 'B' and resid 715 through 732 removed outlier: 3.844A pdb=" N ASN B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 742 removed outlier: 3.881A pdb=" N ILE B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 742 " --> pdb=" O ARG B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 777 removed outlier: 3.820A pdb=" N HIS B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'B' and resid 793 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 820 through 828 removed outlier: 3.628A pdb=" N ASN B 828 " --> pdb=" O LYS B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 849 through 852 removed outlier: 3.730A pdb=" N PHE B 852 " --> pdb=" O GLU B 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 849 through 852' Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 877 through 889 Processing helix chain 'B' and resid 897 through 903 Processing helix chain 'B' and resid 917 through 937 Proline residue: B 923 - end of helix Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'B' and resid 953 through 956 removed outlier: 3.554A pdb=" N PHE B 956 " --> pdb=" O SER B 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 953 through 956' Processing helix chain 'B' and resid 957 through 969 removed outlier: 4.007A pdb=" N THR B 961 " --> pdb=" O ASN B 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 101 through 132 removed outlier: 3.871A pdb=" N MET C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.506A pdb=" N THR C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.527A pdb=" N ALA C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 330 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 341 through 372 removed outlier: 3.877A pdb=" N GLY C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Proline residue: C 381 - end of helix Processing helix chain 'C' and resid 395 through 407 Processing helix chain 'C' and resid 411 through 421 removed outlier: 3.636A pdb=" N ARG C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.716A pdb=" N ALA C 434 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 435 " --> pdb=" O PRO C 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 431 through 435' Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 447 through 470 Processing helix chain 'C' and resid 473 through 485 removed outlier: 3.646A pdb=" N LEU C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 588 Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.615A pdb=" N VAL C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.576A pdb=" N TRP C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 648 through 653 removed outlier: 4.347A pdb=" N TRP C 651 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 665 removed outlier: 3.938A pdb=" N LYS C 663 " --> pdb=" O GLU C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 694 removed outlier: 3.541A pdb=" N ASN C 681 " --> pdb=" O ALA C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 732 removed outlier: 3.792A pdb=" N ASN C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 742 Processing helix chain 'C' and resid 757 through 776 Processing helix chain 'C' and resid 793 through 801 Processing helix chain 'C' and resid 802 through 804 No H-bonds generated for 'chain 'C' and resid 802 through 804' Processing helix chain 'C' and resid 820 through 828 removed outlier: 3.566A pdb=" N ASN C 828 " --> pdb=" O LYS C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 848 Processing helix chain 'C' and resid 858 through 871 removed outlier: 3.887A pdb=" N ALA C 863 " --> pdb=" O ALA C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 888 Processing helix chain 'C' and resid 897 through 903 removed outlier: 3.555A pdb=" N SER C 903 " --> pdb=" O ASP C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 937 Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 938 through 952 Processing helix chain 'C' and resid 957 through 969 removed outlier: 3.986A pdb=" N THR C 961 " --> pdb=" O ASN C 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437 removed outlier: 6.604A pdb=" N TRP A 135 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASP A 311 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 98 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLN A 136 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 100 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLN A 483 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N MET A 539 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 485 " --> pdb=" O MET A 539 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR A 541 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 458 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR A 486 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 460 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 359 removed outlier: 5.955A pdb=" N SER A 342 " --> pdb=" O TRP A 356 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER A 358 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE A 340 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 343 " --> pdb=" O TRP A 400 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRP A 400 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 435 through 437 removed outlier: 6.604A pdb=" N TRP D 135 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP D 311 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA D 98 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLN D 136 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL D 100 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG D 97 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL D 540 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY D 99 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN D 483 " --> pdb=" O THR D 537 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N MET D 539 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 485 " --> pdb=" O MET D 539 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR D 541 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY D 458 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR D 486 " --> pdb=" O GLY D 458 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA D 460 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 359 removed outlier: 6.081A pdb=" N SER D 342 " --> pdb=" O TRP D 356 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER D 358 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE D 340 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 343 " --> pdb=" O TRP D 400 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP D 400 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 245 through 256 removed outlier: 4.244A pdb=" N ALA B 280 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASP B 249 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL B 278 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N SER B 251 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 10.862A pdb=" N ILE B 276 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N GLU B 274 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA B 208 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ARG B 297 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY B 210 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP B 299 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY B 212 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR B 301 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ASN B 592 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 425 " --> pdb=" O ASN B 592 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 591 " --> pdb=" O GLN B 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 221 through 225 Processing sheet with id=AA7, first strand: chain 'B' and resid 259 through 262 Processing sheet with id=AA8, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AA9, first strand: chain 'B' and resid 784 through 788 removed outlier: 6.328A pdb=" N MET B 702 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE B 748 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 704 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLY B 750 " --> pdb=" O ASP B 704 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN B 706 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL B 707 " --> pdb=" O GLN B 808 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 832 " --> pdb=" O PHE B 853 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 245 through 256 removed outlier: 4.222A pdb=" N ALA C 280 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASP C 249 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N VAL C 278 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N SER C 251 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N ILE C 276 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N GLU C 274 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C 208 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ARG C 297 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY C 210 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TRP C 299 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY C 212 " --> pdb=" O TRP C 299 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR C 301 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 389 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 426 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N ASN C 592 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR C 425 " --> pdb=" O ASN C 592 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 591 " --> pdb=" O GLN C 619 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 221 through 225 Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AB4, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.509A pdb=" N VAL C 577 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 784 through 788 removed outlier: 6.285A pdb=" N MET C 702 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE C 748 " --> pdb=" O MET C 702 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 704 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLY C 750 " --> pdb=" O ASP C 704 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN C 706 " --> pdb=" O GLY C 750 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL C 707 " --> pdb=" O GLN C 808 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3669 1.31 - 1.44: 5949 1.44 - 1.57: 12439 1.57 - 1.69: 0 1.69 - 1.82: 152 Bond restraints: 22209 Sorted by residual: bond pdb=" C THR B 820 " pdb=" O THR B 820 " ideal model delta sigma weight residual 1.235 1.188 0.048 1.31e-02 5.83e+03 1.31e+01 bond pdb=" N ILE B 631 " pdb=" CA ILE B 631 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.28e-02 6.10e+03 1.11e+01 bond pdb=" CA SER B 818 " pdb=" CB SER B 818 " ideal model delta sigma weight residual 1.532 1.477 0.056 1.68e-02 3.54e+03 1.09e+01 bond pdb=" N THR C 92 " pdb=" CA THR C 92 " ideal model delta sigma weight residual 1.457 1.485 -0.029 9.10e-03 1.21e+04 9.93e+00 bond pdb=" N VAL C 261 " pdb=" CA VAL C 261 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.40e+00 ... (remaining 22204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 29202 1.71 - 3.42: 739 3.42 - 5.13: 144 5.13 - 6.84: 19 6.84 - 8.55: 2 Bond angle restraints: 30106 Sorted by residual: angle pdb=" CA PHE C 886 " pdb=" CB PHE C 886 " pdb=" CG PHE C 886 " ideal model delta sigma weight residual 113.80 119.52 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CB GLU D 92 " pdb=" CG GLU D 92 " pdb=" CD GLU D 92 " ideal model delta sigma weight residual 112.60 121.15 -8.55 1.70e+00 3.46e-01 2.53e+01 angle pdb=" CA SER B 818 " pdb=" C SER B 818 " pdb=" O SER B 818 " ideal model delta sigma weight residual 121.38 116.12 5.26 1.06e+00 8.90e-01 2.47e+01 angle pdb=" N ILE C 496 " pdb=" CA ILE C 496 " pdb=" C ILE C 496 " ideal model delta sigma weight residual 112.29 107.65 4.64 9.40e-01 1.13e+00 2.44e+01 angle pdb=" C PHE C 91 " pdb=" CA PHE C 91 " pdb=" CB PHE C 91 " ideal model delta sigma weight residual 109.83 118.33 -8.50 1.75e+00 3.27e-01 2.36e+01 ... (remaining 30101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11521 17.97 - 35.93: 1310 35.93 - 53.90: 310 53.90 - 71.87: 92 71.87 - 89.83: 21 Dihedral angle restraints: 13254 sinusoidal: 5373 harmonic: 7881 Sorted by residual: dihedral pdb=" CA THR B 92 " pdb=" C THR B 92 " pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta harmonic sigma weight residual 180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY B 872 " pdb=" C GLY B 872 " pdb=" N LYS B 873 " pdb=" CA LYS B 873 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA HIS B 809 " pdb=" C HIS B 809 " pdb=" N ILE B 810 " pdb=" CA ILE B 810 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 13251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2528 0.051 - 0.103: 600 0.103 - 0.154: 104 0.154 - 0.205: 14 0.205 - 0.256: 4 Chirality restraints: 3250 Sorted by residual: chirality pdb=" CA HIS C 87 " pdb=" N HIS C 87 " pdb=" C HIS C 87 " pdb=" CB HIS C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL C 94 " pdb=" N VAL C 94 " pdb=" C VAL C 94 " pdb=" CB VAL C 94 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA THR B 820 " pdb=" N THR B 820 " pdb=" C THR B 820 " pdb=" CB THR B 820 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3247 not shown) Planarity restraints: 3889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 738 " 0.284 9.50e-02 1.11e+02 1.27e-01 9.91e+00 pdb=" NE ARG C 738 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 738 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 738 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 738 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 629 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.88e+00 pdb=" NE ARG B 629 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 629 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 629 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 629 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 625 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C VAL B 625 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL B 625 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 626 " 0.017 2.00e-02 2.50e+03 ... (remaining 3886 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 7763 2.88 - 3.38: 19854 3.38 - 3.89: 36433 3.89 - 4.39: 42620 4.39 - 4.90: 70456 Nonbonded interactions: 177126 Sorted by model distance: nonbonded pdb=" NE2 HIS C 88 " pdb=" OD2 ASP C 115 " model vdw 2.374 3.120 nonbonded pdb=" O ASP C 390 " pdb=" OG1 THR C 391 " model vdw 2.409 3.040 nonbonded pdb=" O PHE C 91 " pdb=" OG1 THR C 92 " model vdw 2.446 3.040 nonbonded pdb=" O GLN A 560 " pdb=" OE1 GLN A 560 " model vdw 2.451 3.040 nonbonded pdb=" O GLN C 929 " pdb=" OD1 ASP C 933 " model vdw 2.452 3.040 ... (remaining 177121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 77 through 507 or resid 575 through 978)) selection = (chain 'C' and (resid 77 through 507 or resid 575 through 978)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.220 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.007 0.863 22210 Z= 0.389 Angle : 0.679 27.454 30108 Z= 0.414 Chirality : 0.046 0.256 3250 Planarity : 0.006 0.127 3889 Dihedral : 16.601 89.833 8177 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.22 % Allowed : 20.03 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2709 helix: 1.00 (0.14), residues: 1347 sheet: 0.12 (0.29), residues: 322 loop : -0.54 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 94 TYR 0.022 0.002 TYR C 257 PHE 0.016 0.002 PHE C 220 TRP 0.018 0.002 TRP A 524 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00461 (22209) covalent geometry : angle 0.65879 (30106) SS BOND : bond 0.86273 ( 1) SS BOND : angle 20.17029 ( 2) hydrogen bonds : bond 0.17837 ( 1069) hydrogen bonds : angle 5.94214 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.827 Fit side-chains REVERT: A 224 ASP cc_start: 0.7353 (m-30) cc_final: 0.7040 (m-30) REVERT: A 445 GLU cc_start: 0.7464 (tt0) cc_final: 0.7173 (mp0) REVERT: A 539 MET cc_start: 0.8188 (tpp) cc_final: 0.7827 (mmm) REVERT: D 222 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7266 (mt0) REVERT: D 224 ASP cc_start: 0.7613 (m-30) cc_final: 0.7108 (m-30) REVERT: D 237 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7000 (tm-30) REVERT: D 267 ARG cc_start: 0.8144 (tmt-80) cc_final: 0.7892 (tmt-80) REVERT: D 334 LYS cc_start: 0.8634 (pttt) cc_final: 0.8278 (mtmm) REVERT: D 428 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7580 (ttmm) REVERT: D 455 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6882 (mp0) REVERT: D 494 THR cc_start: 0.7221 (m) cc_final: 0.6718 (p) REVERT: D 539 MET cc_start: 0.8280 (tpp) cc_final: 0.7885 (mmm) REVERT: D 542 MET cc_start: 0.7643 (tpt) cc_final: 0.6936 (tpt) REVERT: B 164 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6360 (mm-30) REVERT: B 650 ASP cc_start: 0.8237 (t70) cc_final: 0.7767 (t0) REVERT: B 669 ASP cc_start: 0.7667 (m-30) cc_final: 0.7285 (p0) REVERT: B 898 ASP cc_start: 0.8435 (m-30) cc_final: 0.8113 (t70) REVERT: C 174 GLU cc_start: 0.7832 (mp0) cc_final: 0.7576 (mp0) REVERT: C 462 MET cc_start: 0.7478 (mmp) cc_final: 0.7226 (mtt) REVERT: C 730 MET cc_start: 0.8499 (mtt) cc_final: 0.8248 (mtt) REVERT: C 899 ASP cc_start: 0.8142 (m-30) cc_final: 0.7238 (p0) outliers start: 5 outliers final: 0 residues processed: 199 average time/residue: 0.7258 time to fit residues: 161.8121 Evaluate side-chains 183 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 168 GLN C 740 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094547 restraints weight = 27172.274| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.88 r_work: 0.3010 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22210 Z= 0.143 Angle : 0.526 6.945 30108 Z= 0.283 Chirality : 0.042 0.154 3250 Planarity : 0.004 0.053 3889 Dihedral : 4.326 22.102 2949 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.34 % Allowed : 18.78 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2709 helix: 1.27 (0.14), residues: 1353 sheet: 0.15 (0.29), residues: 316 loop : -0.53 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 267 TYR 0.018 0.002 TYR C 257 PHE 0.015 0.002 PHE C 220 TRP 0.014 0.001 TRP B 630 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00322 (22209) covalent geometry : angle 0.52544 (30106) SS BOND : bond 0.00091 ( 1) SS BOND : angle 2.87306 ( 2) hydrogen bonds : bond 0.05836 ( 1069) hydrogen bonds : angle 4.63685 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.857 Fit side-chains REVERT: A 119 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6164 (mt-10) REVERT: A 281 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 445 GLU cc_start: 0.7519 (tt0) cc_final: 0.7212 (mp0) REVERT: A 539 MET cc_start: 0.8121 (tpp) cc_final: 0.7765 (mmm) REVERT: D 222 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7231 (mt0) REVERT: D 224 ASP cc_start: 0.7598 (m-30) cc_final: 0.7036 (m-30) REVERT: D 237 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7032 (tm-30) REVERT: D 267 ARG cc_start: 0.7634 (tmt-80) cc_final: 0.7158 (ttp-110) REVERT: D 272 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8440 (tt) REVERT: D 303 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7919 (ttpp) REVERT: D 334 LYS cc_start: 0.8625 (pttt) cc_final: 0.8244 (mtmm) REVERT: D 366 MET cc_start: 0.7488 (mtp) cc_final: 0.7001 (mtt) REVERT: D 391 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: D 428 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7541 (ttmm) REVERT: D 455 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6606 (mp0) REVERT: D 494 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6769 (p) REVERT: D 539 MET cc_start: 0.8215 (tpp) cc_final: 0.7921 (mmm) REVERT: B 164 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6365 (mm-30) REVERT: B 230 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 420 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: B 507 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7200 (mttt) REVERT: B 650 ASP cc_start: 0.8117 (t70) cc_final: 0.7711 (t0) REVERT: B 669 ASP cc_start: 0.7671 (m-30) cc_final: 0.7322 (p0) REVERT: B 898 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8063 (t70) REVERT: B 960 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7872 (ttm110) REVERT: C 174 GLU cc_start: 0.7841 (mp0) cc_final: 0.7594 (mp0) REVERT: C 230 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8048 (mm-30) REVERT: C 306 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: C 462 MET cc_start: 0.7427 (mmp) cc_final: 0.7200 (mtt) REVERT: C 650 ASP cc_start: 0.8110 (t0) cc_final: 0.7705 (t0) outliers start: 54 outliers final: 24 residues processed: 231 average time/residue: 0.6927 time to fit residues: 180.0266 Evaluate side-chains 216 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 125 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 265 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 740 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.094738 restraints weight = 27102.021| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.89 r_work: 0.3014 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22210 Z= 0.175 Angle : 0.549 6.601 30108 Z= 0.295 Chirality : 0.043 0.206 3250 Planarity : 0.004 0.051 3889 Dihedral : 4.443 22.381 2949 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.73 % Allowed : 18.13 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2709 helix: 1.31 (0.14), residues: 1340 sheet: 0.15 (0.29), residues: 316 loop : -0.52 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 366 TYR 0.021 0.002 TYR C 257 PHE 0.018 0.002 PHE C 220 TRP 0.014 0.002 TRP B 121 HIS 0.006 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00409 (22209) covalent geometry : angle 0.54870 (30106) SS BOND : bond 0.00925 ( 1) SS BOND : angle 1.93072 ( 2) hydrogen bonds : bond 0.06243 ( 1069) hydrogen bonds : angle 4.51935 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 0.878 Fit side-chains REVERT: A 119 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6180 (mt-10) REVERT: A 182 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: A 281 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 411 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7640 (p) REVERT: A 445 GLU cc_start: 0.7609 (tt0) cc_final: 0.7194 (mp0) REVERT: A 539 MET cc_start: 0.8099 (tpp) cc_final: 0.7735 (mmm) REVERT: D 195 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7530 (p0) REVERT: D 222 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7180 (mt0) REVERT: D 224 ASP cc_start: 0.7638 (m-30) cc_final: 0.7037 (m-30) REVERT: D 267 ARG cc_start: 0.7702 (tmt-80) cc_final: 0.7221 (ttp-110) REVERT: D 272 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8462 (tt) REVERT: D 303 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7946 (ttpp) REVERT: D 334 LYS cc_start: 0.8595 (pttt) cc_final: 0.8203 (mtmm) REVERT: D 428 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7534 (ttmm) REVERT: D 494 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6804 (p) REVERT: D 539 MET cc_start: 0.8249 (tpp) cc_final: 0.7944 (mmm) REVERT: B 164 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6288 (mm-30) REVERT: B 230 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 306 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8732 (pt0) REVERT: B 420 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 650 ASP cc_start: 0.8136 (t70) cc_final: 0.7708 (t0) REVERT: B 669 ASP cc_start: 0.7736 (m-30) cc_final: 0.7389 (p0) REVERT: B 898 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8041 (t70) REVERT: B 960 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7933 (ttm110) REVERT: C 174 GLU cc_start: 0.7848 (mp0) cc_final: 0.7603 (mp0) REVERT: C 306 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (pt0) REVERT: C 650 ASP cc_start: 0.8125 (t0) cc_final: 0.7705 (t0) outliers start: 63 outliers final: 26 residues processed: 237 average time/residue: 0.6996 time to fit residues: 186.5405 Evaluate side-chains 221 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 201 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097624 restraints weight = 27021.216| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.90 r_work: 0.3059 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22210 Z= 0.112 Angle : 0.479 10.005 30108 Z= 0.256 Chirality : 0.041 0.195 3250 Planarity : 0.003 0.050 3889 Dihedral : 4.139 21.200 2949 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 18.48 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2709 helix: 1.55 (0.14), residues: 1358 sheet: 0.29 (0.30), residues: 312 loop : -0.45 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 366 TYR 0.013 0.001 TYR C 353 PHE 0.012 0.001 PHE B 220 TRP 0.013 0.001 TRP B 630 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00245 (22209) covalent geometry : angle 0.47930 (30106) SS BOND : bond 0.00493 ( 1) SS BOND : angle 1.14092 ( 2) hydrogen bonds : bond 0.04835 ( 1069) hydrogen bonds : angle 4.27632 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 0.840 Fit side-chains REVERT: A 182 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: A 281 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 411 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7604 (p) REVERT: A 445 GLU cc_start: 0.7609 (tt0) cc_final: 0.7180 (mp0) REVERT: A 539 MET cc_start: 0.8118 (tpp) cc_final: 0.7738 (mmm) REVERT: D 190 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: D 222 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7244 (mt0) REVERT: D 224 ASP cc_start: 0.7590 (m-30) cc_final: 0.7043 (m-30) REVERT: D 267 ARG cc_start: 0.7654 (tmt-80) cc_final: 0.7190 (ttp-110) REVERT: D 272 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8426 (tt) REVERT: D 303 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: D 334 LYS cc_start: 0.8603 (pttt) cc_final: 0.8203 (mtmm) REVERT: D 391 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: D 428 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7432 (ttmm) REVERT: D 494 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6665 (p) REVERT: D 539 MET cc_start: 0.8250 (tpp) cc_final: 0.7931 (mmm) REVERT: B 164 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6304 (mm-30) REVERT: B 230 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 306 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: B 420 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: B 650 ASP cc_start: 0.8118 (t70) cc_final: 0.7632 (t0) REVERT: B 669 ASP cc_start: 0.7597 (m-30) cc_final: 0.7284 (p0) REVERT: B 898 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8029 (t70) REVERT: B 960 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7762 (ttm110) REVERT: C 174 GLU cc_start: 0.7820 (mp0) cc_final: 0.7575 (mp0) REVERT: C 230 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 604 GLU cc_start: 0.7979 (pt0) cc_final: 0.7716 (mm-30) REVERT: C 650 ASP cc_start: 0.8123 (t0) cc_final: 0.7681 (t0) outliers start: 58 outliers final: 19 residues processed: 236 average time/residue: 0.6926 time to fit residues: 184.0276 Evaluate side-chains 215 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 250 optimal weight: 5.9990 chunk 50 optimal weight: 0.0570 chunk 114 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096539 restraints weight = 27000.051| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.89 r_work: 0.3041 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22210 Z= 0.132 Angle : 0.498 5.833 30108 Z= 0.267 Chirality : 0.041 0.185 3250 Planarity : 0.004 0.048 3889 Dihedral : 4.169 21.144 2949 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.42 % Allowed : 19.00 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2709 helix: 1.55 (0.14), residues: 1358 sheet: 0.27 (0.30), residues: 314 loop : -0.43 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 366 TYR 0.016 0.001 TYR B 353 PHE 0.020 0.001 PHE C 100 TRP 0.013 0.001 TRP D 499 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00300 (22209) covalent geometry : angle 0.49716 (30106) SS BOND : bond 0.01308 ( 1) SS BOND : angle 3.31522 ( 2) hydrogen bonds : bond 0.05187 ( 1069) hydrogen bonds : angle 4.26285 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.687 Fit side-chains REVERT: A 182 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 281 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7275 (mm-30) REVERT: A 411 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 539 MET cc_start: 0.8129 (tpp) cc_final: 0.7751 (mmm) REVERT: D 190 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: D 195 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7525 (p0) REVERT: D 222 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7288 (mt0) REVERT: D 224 ASP cc_start: 0.7598 (m-30) cc_final: 0.7047 (m-30) REVERT: D 267 ARG cc_start: 0.7659 (tmt-80) cc_final: 0.7181 (ttp-110) REVERT: D 272 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8447 (tt) REVERT: D 303 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7881 (ttpp) REVERT: D 334 LYS cc_start: 0.8600 (pttt) cc_final: 0.8201 (mtmm) REVERT: D 391 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: D 428 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7444 (ttmm) REVERT: D 494 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6671 (p) REVERT: D 539 MET cc_start: 0.8218 (tpp) cc_final: 0.7925 (mmm) REVERT: B 164 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6274 (mm-30) REVERT: B 230 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 306 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: B 420 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: B 507 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7147 (mttt) REVERT: B 650 ASP cc_start: 0.8107 (t70) cc_final: 0.7608 (t0) REVERT: B 669 ASP cc_start: 0.7630 (m-30) cc_final: 0.7311 (p0) REVERT: B 898 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8057 (t70) REVERT: B 960 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7846 (ttm110) REVERT: C 174 GLU cc_start: 0.7832 (mp0) cc_final: 0.7585 (mp0) REVERT: C 230 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7911 (mm-30) REVERT: C 604 GLU cc_start: 0.7988 (pt0) cc_final: 0.7730 (mm-30) REVERT: C 650 ASP cc_start: 0.8161 (t0) cc_final: 0.7702 (t0) outliers start: 56 outliers final: 26 residues processed: 228 average time/residue: 0.7073 time to fit residues: 181.9714 Evaluate side-chains 224 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 306 GLN C 389 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.092757 restraints weight = 27102.611| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.89 r_work: 0.2983 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22210 Z= 0.254 Angle : 0.620 7.040 30108 Z= 0.334 Chirality : 0.047 0.197 3250 Planarity : 0.005 0.044 3889 Dihedral : 4.682 27.935 2949 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.03 % Allowed : 18.61 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2709 helix: 1.12 (0.14), residues: 1356 sheet: 0.25 (0.30), residues: 306 loop : -0.63 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 726 TYR 0.022 0.002 TYR C 257 PHE 0.019 0.002 PHE B 220 TRP 0.016 0.002 TRP D 498 HIS 0.008 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00615 (22209) covalent geometry : angle 0.61967 (30106) SS BOND : bond 0.01706 ( 1) SS BOND : angle 3.04538 ( 2) hydrogen bonds : bond 0.07175 ( 1069) hydrogen bonds : angle 4.55988 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 184 time to evaluate : 0.843 Fit side-chains REVERT: A 182 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: A 281 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7230 (mm-30) REVERT: A 411 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7631 (p) REVERT: D 165 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7522 (mp) REVERT: D 190 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: D 195 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7474 (p0) REVERT: D 222 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7263 (mt0) REVERT: D 224 ASP cc_start: 0.7659 (m-30) cc_final: 0.7032 (m-30) REVERT: D 267 ARG cc_start: 0.7721 (tmt-80) cc_final: 0.7198 (ttp-110) REVERT: D 272 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8466 (tt) REVERT: D 303 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7900 (ttpp) REVERT: D 334 LYS cc_start: 0.8591 (pttt) cc_final: 0.8212 (mtmm) REVERT: D 428 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7545 (ttmm) REVERT: D 494 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.6879 (p) REVERT: D 539 MET cc_start: 0.8232 (tpp) cc_final: 0.8002 (mmm) REVERT: B 164 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6371 (mm-30) REVERT: B 420 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 507 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7251 (mttt) REVERT: B 650 ASP cc_start: 0.8168 (t70) cc_final: 0.7729 (t0) REVERT: B 730 MET cc_start: 0.8622 (mtt) cc_final: 0.8393 (mtt) REVERT: B 898 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8049 (t70) REVERT: B 960 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7977 (ttm110) REVERT: C 306 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8748 (pt0) REVERT: C 482 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7747 (mptt) REVERT: C 506 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7820 (tmtt) REVERT: C 604 GLU cc_start: 0.8059 (pt0) cc_final: 0.7745 (mm-30) REVERT: C 650 ASP cc_start: 0.8160 (t0) cc_final: 0.7727 (t0) outliers start: 70 outliers final: 30 residues processed: 241 average time/residue: 0.7390 time to fit residues: 199.5067 Evaluate side-chains 226 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095131 restraints weight = 27288.007| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.88 r_work: 0.3019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22210 Z= 0.114 Angle : 0.496 6.847 30108 Z= 0.265 Chirality : 0.041 0.165 3250 Planarity : 0.004 0.046 3889 Dihedral : 4.257 24.636 2949 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 19.86 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2709 helix: 1.51 (0.14), residues: 1358 sheet: 0.23 (0.30), residues: 312 loop : -0.48 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 108 TYR 0.014 0.001 TYR B 353 PHE 0.022 0.001 PHE C 100 TRP 0.014 0.001 TRP A 524 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00247 (22209) covalent geometry : angle 0.49607 (30106) SS BOND : bond 0.00828 ( 1) SS BOND : angle 2.03749 ( 2) hydrogen bonds : bond 0.04997 ( 1069) hydrogen bonds : angle 4.27308 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.815 Fit side-chains REVERT: A 281 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 411 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 539 MET cc_start: 0.8149 (tpp) cc_final: 0.7851 (mmm) REVERT: D 95 ARG cc_start: 0.7411 (ptm160) cc_final: 0.6574 (ptm-80) REVERT: D 190 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: D 222 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7278 (mt0) REVERT: D 224 ASP cc_start: 0.7644 (m-30) cc_final: 0.7037 (m-30) REVERT: D 267 ARG cc_start: 0.7656 (tmt-80) cc_final: 0.7167 (ttp-110) REVERT: D 272 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8452 (tt) REVERT: D 303 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7907 (ttpp) REVERT: D 334 LYS cc_start: 0.8612 (pttt) cc_final: 0.8225 (mtmm) REVERT: D 391 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: D 494 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6785 (p) REVERT: D 539 MET cc_start: 0.8264 (tpp) cc_final: 0.7986 (mmm) REVERT: B 164 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6320 (mm-30) REVERT: B 420 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: B 507 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7185 (mttt) REVERT: B 650 ASP cc_start: 0.8149 (t70) cc_final: 0.7693 (t0) REVERT: B 898 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8035 (t70) REVERT: B 960 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7733 (ttm110) REVERT: C 230 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 482 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7655 (mptt) REVERT: C 506 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7789 (tmtt) REVERT: C 604 GLU cc_start: 0.8018 (pt0) cc_final: 0.7751 (mm-30) REVERT: C 650 ASP cc_start: 0.8165 (t0) cc_final: 0.7709 (t0) outliers start: 48 outliers final: 22 residues processed: 224 average time/residue: 0.7281 time to fit residues: 183.4936 Evaluate side-chains 216 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092970 restraints weight = 27170.732| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.88 r_work: 0.2988 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22210 Z= 0.173 Angle : 0.550 10.039 30108 Z= 0.294 Chirality : 0.043 0.174 3250 Planarity : 0.004 0.064 3889 Dihedral : 4.413 24.326 2949 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.25 % Allowed : 20.21 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2709 helix: 1.38 (0.14), residues: 1356 sheet: 0.21 (0.29), residues: 314 loop : -0.51 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.018 0.002 TYR C 353 PHE 0.018 0.002 PHE C 220 TRP 0.016 0.002 TRP A 524 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00407 (22209) covalent geometry : angle 0.54988 (30106) SS BOND : bond 0.01068 ( 1) SS BOND : angle 2.05803 ( 2) hydrogen bonds : bond 0.05938 ( 1069) hydrogen bonds : angle 4.36236 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 0.894 Fit side-chains REVERT: A 281 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 411 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7591 (p) REVERT: A 539 MET cc_start: 0.8152 (tpp) cc_final: 0.7906 (mmm) REVERT: D 108 ARG cc_start: 0.7276 (ptt180) cc_final: 0.7039 (ptm-80) REVERT: D 190 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: D 222 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7272 (mt0) REVERT: D 224 ASP cc_start: 0.7652 (m-30) cc_final: 0.7014 (m-30) REVERT: D 267 ARG cc_start: 0.7715 (tmt-80) cc_final: 0.7195 (ttp-110) REVERT: D 303 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7892 (ttpp) REVERT: D 334 LYS cc_start: 0.8606 (pttt) cc_final: 0.8219 (mtmm) REVERT: D 391 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: D 428 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7499 (ttmm) REVERT: D 494 THR cc_start: 0.7349 (OUTLIER) cc_final: 0.6826 (p) REVERT: D 539 MET cc_start: 0.8225 (tpp) cc_final: 0.7939 (mmm) REVERT: B 164 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6384 (mm-30) REVERT: B 420 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: B 507 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7208 (mttt) REVERT: B 650 ASP cc_start: 0.8151 (t70) cc_final: 0.7699 (t0) REVERT: B 898 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8034 (t70) REVERT: B 960 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7937 (ttm110) REVERT: C 230 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7942 (mm-30) REVERT: C 482 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7753 (mptt) REVERT: C 506 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7803 (tmtt) REVERT: C 604 GLU cc_start: 0.7960 (pt0) cc_final: 0.7710 (mm-30) REVERT: C 650 ASP cc_start: 0.8169 (t0) cc_final: 0.7713 (t0) outliers start: 52 outliers final: 28 residues processed: 221 average time/residue: 0.6957 time to fit residues: 173.1612 Evaluate side-chains 217 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 2 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 190 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 274 GLN C 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092935 restraints weight = 27046.759| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.89 r_work: 0.2979 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22210 Z= 0.229 Angle : 0.609 11.728 30108 Z= 0.325 Chirality : 0.046 0.181 3250 Planarity : 0.005 0.060 3889 Dihedral : 4.639 24.710 2949 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.29 % Allowed : 20.29 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2709 helix: 1.14 (0.14), residues: 1356 sheet: 0.16 (0.29), residues: 314 loop : -0.59 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 108 TYR 0.021 0.002 TYR B 125 PHE 0.022 0.002 PHE C 100 TRP 0.020 0.002 TRP A 524 HIS 0.008 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00552 (22209) covalent geometry : angle 0.60877 (30106) SS BOND : bond 0.01255 ( 1) SS BOND : angle 2.17446 ( 2) hydrogen bonds : bond 0.06809 ( 1069) hydrogen bonds : angle 4.51549 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.879 Fit side-chains REVERT: A 281 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 411 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7593 (p) REVERT: A 539 MET cc_start: 0.8135 (tpp) cc_final: 0.7886 (mmm) REVERT: D 179 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.4943 (mpm) REVERT: D 190 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: D 222 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7265 (mt0) REVERT: D 224 ASP cc_start: 0.7684 (m-30) cc_final: 0.7046 (m-30) REVERT: D 267 ARG cc_start: 0.7754 (tmt-80) cc_final: 0.7182 (ttp-110) REVERT: D 303 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: D 334 LYS cc_start: 0.8598 (pttt) cc_final: 0.8211 (mtmm) REVERT: D 455 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: D 494 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.6863 (p) REVERT: D 539 MET cc_start: 0.8214 (tpp) cc_final: 0.7988 (mmm) REVERT: B 420 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: B 507 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7266 (mttt) REVERT: B 650 ASP cc_start: 0.8133 (t70) cc_final: 0.7696 (t0) REVERT: B 898 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8004 (t70) REVERT: B 908 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: B 960 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7943 (ttm110) REVERT: C 306 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (pt0) REVERT: C 482 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7754 (mptt) REVERT: C 506 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7789 (tmtt) REVERT: C 604 GLU cc_start: 0.7975 (pt0) cc_final: 0.7701 (mm-30) REVERT: C 650 ASP cc_start: 0.8183 (t0) cc_final: 0.7741 (t0) REVERT: C 730 MET cc_start: 0.8571 (mtt) cc_final: 0.8365 (mtt) outliers start: 53 outliers final: 32 residues processed: 219 average time/residue: 0.7054 time to fit residues: 173.8965 Evaluate side-chains 221 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 269 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095704 restraints weight = 27144.019| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.92 r_work: 0.3036 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22210 Z= 0.117 Angle : 0.504 11.607 30108 Z= 0.267 Chirality : 0.041 0.159 3250 Planarity : 0.004 0.051 3889 Dihedral : 4.232 22.934 2949 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.34 % Allowed : 21.29 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2709 helix: 1.50 (0.14), residues: 1358 sheet: 0.24 (0.30), residues: 311 loop : -0.45 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 370 TYR 0.013 0.001 TYR B 353 PHE 0.012 0.001 PHE C 220 TRP 0.017 0.001 TRP A 524 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00259 (22209) covalent geometry : angle 0.50355 (30106) SS BOND : bond 0.00675 ( 1) SS BOND : angle 1.64786 ( 2) hydrogen bonds : bond 0.04861 ( 1069) hydrogen bonds : angle 4.25937 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.877 Fit side-chains REVERT: A 281 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7170 (mm-30) REVERT: A 411 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 539 MET cc_start: 0.8129 (tpp) cc_final: 0.7808 (mmm) REVERT: D 95 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6415 (ptm-80) REVERT: D 179 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.4918 (mpm) REVERT: D 190 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: D 222 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7266 (mt0) REVERT: D 224 ASP cc_start: 0.7647 (m-30) cc_final: 0.6997 (m-30) REVERT: D 267 ARG cc_start: 0.7637 (tmt-80) cc_final: 0.7100 (ttp-110) REVERT: D 303 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7902 (ttpp) REVERT: D 334 LYS cc_start: 0.8591 (pttt) cc_final: 0.8184 (mtmm) REVERT: D 391 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: D 494 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6764 (p) REVERT: D 539 MET cc_start: 0.8238 (tpp) cc_final: 0.7962 (mmm) REVERT: D 542 MET cc_start: 0.7690 (tpt) cc_final: 0.6942 (tpt) REVERT: B 420 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: B 507 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7163 (mttt) REVERT: B 650 ASP cc_start: 0.8134 (t70) cc_final: 0.7675 (t0) REVERT: B 898 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7998 (t70) REVERT: B 960 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7716 (ttm110) REVERT: C 230 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 482 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7610 (mptt) REVERT: C 506 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7804 (tmtt) REVERT: C 604 GLU cc_start: 0.7927 (pt0) cc_final: 0.7678 (mm-30) REVERT: C 650 ASP cc_start: 0.8151 (t0) cc_final: 0.7687 (t0) outliers start: 31 outliers final: 18 residues processed: 209 average time/residue: 0.7265 time to fit residues: 170.4490 Evaluate side-chains 210 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 394 ARG Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 507 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 960 ARG Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 45 optimal weight: 9.9990 chunk 199 optimal weight: 0.0570 chunk 201 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 107 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098377 restraints weight = 27165.178| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.88 r_work: 0.3069 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 22210 Z= 0.099 Angle : 0.472 11.313 30108 Z= 0.249 Chirality : 0.040 0.153 3250 Planarity : 0.003 0.046 3889 Dihedral : 3.941 22.444 2949 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.34 % Allowed : 21.46 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.17), residues: 2709 helix: 1.79 (0.14), residues: 1351 sheet: 0.16 (0.28), residues: 348 loop : -0.28 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 366 TYR 0.012 0.001 TYR B 138 PHE 0.028 0.001 PHE C 100 TRP 0.015 0.001 TRP D 499 HIS 0.002 0.000 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00214 (22209) covalent geometry : angle 0.47153 (30106) SS BOND : bond 0.00549 ( 1) SS BOND : angle 1.47631 ( 2) hydrogen bonds : bond 0.04041 ( 1069) hydrogen bonds : angle 4.09752 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9989.13 seconds wall clock time: 170 minutes 9.31 seconds (10209.31 seconds total)