Starting phenix.real_space_refine on Mon Jul 28 23:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.map" model { file = "/net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qm6_4589/07_2025/6qm6_4589.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 7056 2.51 5 N 1814 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10852 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5426 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 29, 'TRANS': 642} Chain breaks: 5 Restraints were copied for chains: B Time building chain proxies: 10.53, per 1000 atoms: 0.97 Number of scatterers: 10852 At special positions: 0 Unit cell: (88.044, 141.68, 107.272, 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 40 16.00 O 1942 8.00 N 1814 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 70.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.753A pdb=" N THR A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.776A pdb=" N LYS A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.540A pdb=" N ASN A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.573A pdb=" N SER A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.779A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 244 removed outlier: 3.513A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 290 through 318 removed outlier: 3.554A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.519A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.644A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 4.252A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 removed outlier: 4.154A pdb=" N PHE A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.630A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.504A pdb=" N GLN A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.919A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 4.085A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.623A pdb=" N ASN A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.680A pdb=" N SER A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.584A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 649 removed outlier: 3.540A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.637A pdb=" N ILE A 670 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 718 removed outlier: 3.914A pdb=" N THR A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.753A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.539A pdb=" N ASN B 138 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.573A pdb=" N SER B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 199 removed outlier: 3.779A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 244 removed outlier: 3.513A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.554A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.518A pdb=" N PHE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.644A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 4.252A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 415 removed outlier: 4.153A pdb=" N PHE B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 407 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.630A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.504A pdb=" N GLN B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.919A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 4.086A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.623A pdb=" N ASN B 531 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.681A pdb=" N SER B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.585A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 649 removed outlier: 3.540A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.637A pdb=" N ILE B 670 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 Processing helix chain 'B' and resid 700 through 718 removed outlier: 3.914A pdb=" N THR B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 718 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.576A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.725A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.576A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.724A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3436 1.34 - 1.46: 2295 1.46 - 1.58: 5335 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11132 Sorted by residual: bond pdb=" C SER B 595 " pdb=" N PRO B 596 " ideal model delta sigma weight residual 1.330 1.372 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" C SER A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.23e-02 6.61e+03 1.12e+01 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.01e+00 bond pdb=" N GLU B 32 " pdb=" CA GLU B 32 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.88e+00 ... (remaining 11127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14619 1.98 - 3.97: 400 3.97 - 5.95: 55 5.95 - 7.93: 14 7.93 - 9.91: 8 Bond angle restraints: 15096 Sorted by residual: angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 118.88 124.52 -5.64 1.54e+00 4.22e-01 1.34e+01 angle pdb=" CA ILE B 394 " pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 118.88 124.49 -5.61 1.54e+00 4.22e-01 1.33e+01 angle pdb=" CA GLU A 32 " pdb=" CB GLU A 32 " pdb=" CG GLU A 32 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA GLU B 32 " pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 118.44 123.43 -4.99 1.59e+00 3.96e-01 9.83e+00 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 5737 16.20 - 32.40: 661 32.40 - 48.59: 124 48.59 - 64.79: 20 64.79 - 80.99: 14 Dihedral angle restraints: 6556 sinusoidal: 2636 harmonic: 3920 Sorted by residual: dihedral pdb=" CA HIS B 401 " pdb=" C HIS B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 401 " pdb=" C HIS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PRO A 341 " pdb=" CA PRO A 341 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1283 0.047 - 0.094: 271 0.094 - 0.141: 82 0.141 - 0.188: 18 0.188 - 0.235: 2 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1653 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 402 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 401 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 402 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 595 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO A 596 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.025 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3674 2.85 - 3.36: 10232 3.36 - 3.88: 17348 3.88 - 4.39: 20232 4.39 - 4.90: 34081 Nonbonded interactions: 85567 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.338 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.338 3.040 nonbonded pdb=" O PHE A 528 " pdb=" ND2 ASN A 532 " model vdw 2.376 3.120 nonbonded pdb=" O PHE B 528 " pdb=" ND2 ASN B 532 " model vdw 2.376 3.120 nonbonded pdb=" O GLN A 374 " pdb=" ND2 ASN A 378 " model vdw 2.382 3.120 ... (remaining 85562 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.040 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.004 0.058 11132 Z= 0.207 Angle : 0.844 9.915 15096 Z= 0.500 Chirality : 0.045 0.235 1656 Planarity : 0.006 0.068 1916 Dihedral : 14.338 80.989 4012 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.14), residues: 1320 helix: -4.55 (0.06), residues: 874 sheet: -2.94 (0.54), residues: 50 loop : -1.98 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 235 HIS 0.005 0.001 HIS A 479 PHE 0.021 0.001 PHE A 205 TYR 0.015 0.001 TYR B 26 ARG 0.002 0.000 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.30865 ( 601) hydrogen bonds : angle 10.15334 ( 1797) covalent geometry : bond 0.00439 (11132) covalent geometry : angle 0.84357 (15096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.9496 (t80) cc_final: 0.9094 (t80) REVERT: A 211 LEU cc_start: 0.9046 (tp) cc_final: 0.8834 (tt) REVERT: A 286 LYS cc_start: 0.7578 (mttt) cc_final: 0.6672 (mmtt) REVERT: A 507 MET cc_start: 0.8684 (mmp) cc_final: 0.8173 (mmt) REVERT: B 211 LEU cc_start: 0.9074 (tp) cc_final: 0.8835 (tt) REVERT: B 286 LYS cc_start: 0.7415 (mttt) cc_final: 0.6536 (mmtt) REVERT: B 357 MET cc_start: 0.8451 (mtp) cc_final: 0.8234 (ttm) REVERT: B 507 MET cc_start: 0.8816 (mmp) cc_final: 0.8361 (mmt) REVERT: B 693 MET cc_start: 0.7774 (ppp) cc_final: 0.7475 (tmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2323 time to fit residues: 72.1238 Evaluate side-chains 151 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.0470 chunk 78 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 42 GLN A 98 HIS A 99 ASN A 143 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 461 GLN A 510 GLN A 532 ASN B 17 ASN B 98 HIS B 99 ASN B 143 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS B 461 GLN B 510 GLN B 532 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.081211 restraints weight = 19964.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.083696 restraints weight = 10592.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085360 restraints weight = 7368.507| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11132 Z= 0.171 Angle : 0.612 7.251 15096 Z= 0.321 Chirality : 0.040 0.181 1656 Planarity : 0.005 0.041 1916 Dihedral : 4.440 16.863 1444 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.95 % Allowed : 12.82 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.19), residues: 1320 helix: -1.80 (0.14), residues: 896 sheet: -1.06 (0.57), residues: 62 loop : -1.60 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 141 HIS 0.005 0.001 HIS B 58 PHE 0.025 0.001 PHE A 315 TYR 0.015 0.001 TYR A 26 ARG 0.004 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 601) hydrogen bonds : angle 4.44945 ( 1797) covalent geometry : bond 0.00379 (11132) covalent geometry : angle 0.61247 (15096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8369 (mtt-85) REVERT: A 205 PHE cc_start: 0.8669 (p90) cc_final: 0.8445 (p90) REVERT: A 211 LEU cc_start: 0.9099 (tp) cc_final: 0.8844 (tt) REVERT: A 268 GLU cc_start: 0.7641 (tp30) cc_final: 0.7205 (tp30) REVERT: A 274 GLU cc_start: 0.8332 (tt0) cc_final: 0.7517 (tm-30) REVERT: A 277 LYS cc_start: 0.9018 (mttt) cc_final: 0.8547 (mmtp) REVERT: A 286 LYS cc_start: 0.7500 (mttt) cc_final: 0.6682 (tttt) REVERT: A 298 CYS cc_start: 0.8405 (m) cc_final: 0.8182 (m) REVERT: B 211 LEU cc_start: 0.9148 (tp) cc_final: 0.8878 (tt) REVERT: B 268 GLU cc_start: 0.7693 (tp30) cc_final: 0.7218 (tp30) REVERT: B 274 GLU cc_start: 0.8238 (tt0) cc_final: 0.7679 (tm-30) REVERT: B 277 LYS cc_start: 0.8987 (mttt) cc_final: 0.8545 (mmtp) REVERT: B 286 LYS cc_start: 0.7447 (mttt) cc_final: 0.6610 (tttt) REVERT: B 298 CYS cc_start: 0.8375 (m) cc_final: 0.8144 (m) REVERT: B 635 GLU cc_start: 0.8608 (tp30) cc_final: 0.8378 (tp30) outliers start: 11 outliers final: 6 residues processed: 193 average time/residue: 0.2674 time to fit residues: 75.8685 Evaluate side-chains 169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 378 ASN A 532 ASN A 666 HIS B 378 ASN B 532 ASN B 666 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.081574 restraints weight = 20034.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.084108 restraints weight = 10602.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.085717 restraints weight = 7343.701| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11132 Z= 0.147 Angle : 0.566 7.340 15096 Z= 0.288 Chirality : 0.040 0.181 1656 Planarity : 0.004 0.034 1916 Dihedral : 4.091 15.280 1444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.39 % Allowed : 15.08 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1320 helix: -0.28 (0.17), residues: 906 sheet: -0.21 (0.64), residues: 58 loop : -1.35 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.004 0.001 HIS A 58 PHE 0.027 0.001 PHE B 315 TYR 0.015 0.001 TYR A 26 ARG 0.002 0.000 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 601) hydrogen bonds : angle 3.88893 ( 1797) covalent geometry : bond 0.00336 (11132) covalent geometry : angle 0.56613 (15096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: A 211 LEU cc_start: 0.9153 (tp) cc_final: 0.8842 (tt) REVERT: A 268 GLU cc_start: 0.7606 (tp30) cc_final: 0.7152 (tp30) REVERT: A 286 LYS cc_start: 0.7684 (mttt) cc_final: 0.6866 (tttt) REVERT: A 457 TYR cc_start: 0.6276 (t80) cc_final: 0.5883 (t80) REVERT: A 701 MET cc_start: 0.7835 (ptt) cc_final: 0.5687 (ttp) REVERT: B 45 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7975 (ttm-80) REVERT: B 211 LEU cc_start: 0.9154 (tp) cc_final: 0.8862 (tt) REVERT: B 268 GLU cc_start: 0.7718 (tp30) cc_final: 0.7393 (tp30) REVERT: B 286 LYS cc_start: 0.7582 (mttt) cc_final: 0.6778 (tttt) REVERT: B 298 CYS cc_start: 0.8386 (m) cc_final: 0.8136 (m) REVERT: B 457 TYR cc_start: 0.6092 (t80) cc_final: 0.5796 (t80) REVERT: B 597 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8483 (pp) outliers start: 16 outliers final: 8 residues processed: 182 average time/residue: 0.1961 time to fit residues: 53.7337 Evaluate side-chains 170 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.111658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.083413 restraints weight = 19867.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086026 restraints weight = 10570.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087649 restraints weight = 7323.718| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11132 Z= 0.113 Angle : 0.540 11.507 15096 Z= 0.269 Chirality : 0.039 0.193 1656 Planarity : 0.004 0.035 1916 Dihedral : 3.868 13.311 1444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.30 % Allowed : 16.55 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1320 helix: 0.60 (0.18), residues: 906 sheet: -0.10 (0.68), residues: 58 loop : -1.16 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 227 HIS 0.005 0.001 HIS B 58 PHE 0.024 0.001 PHE B 315 TYR 0.015 0.001 TYR B 26 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 601) hydrogen bonds : angle 3.56284 ( 1797) covalent geometry : bond 0.00255 (11132) covalent geometry : angle 0.54023 (15096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8276 (mtt-85) REVERT: A 211 LEU cc_start: 0.9146 (tp) cc_final: 0.8793 (tt) REVERT: A 241 ASP cc_start: 0.8188 (t0) cc_final: 0.7942 (t0) REVERT: A 268 GLU cc_start: 0.7587 (tp30) cc_final: 0.7328 (tp30) REVERT: A 298 CYS cc_start: 0.8098 (m) cc_final: 0.7767 (m) REVERT: A 457 TYR cc_start: 0.5978 (t80) cc_final: 0.5685 (t80) REVERT: A 693 MET cc_start: 0.7526 (ppp) cc_final: 0.7307 (tmm) REVERT: A 701 MET cc_start: 0.7678 (ptt) cc_final: 0.7437 (ttp) REVERT: B 211 LEU cc_start: 0.9144 (tp) cc_final: 0.8808 (tt) REVERT: B 268 GLU cc_start: 0.7649 (tp30) cc_final: 0.7401 (tp30) REVERT: B 274 GLU cc_start: 0.8083 (tt0) cc_final: 0.7694 (tm-30) REVERT: B 286 LYS cc_start: 0.7625 (mttt) cc_final: 0.6838 (tttt) REVERT: B 298 CYS cc_start: 0.8281 (m) cc_final: 0.8020 (m) REVERT: B 693 MET cc_start: 0.7598 (ppp) cc_final: 0.7342 (ppp) outliers start: 15 outliers final: 11 residues processed: 184 average time/residue: 0.2003 time to fit residues: 56.8047 Evaluate side-chains 171 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.111465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.083596 restraints weight = 19956.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.086175 restraints weight = 10509.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.087802 restraints weight = 7253.561| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11132 Z= 0.118 Angle : 0.567 11.965 15096 Z= 0.276 Chirality : 0.039 0.187 1656 Planarity : 0.004 0.053 1916 Dihedral : 3.792 13.790 1444 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 17.68 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1320 helix: 1.03 (0.18), residues: 908 sheet: -0.10 (0.70), residues: 58 loop : -1.03 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 600 HIS 0.004 0.001 HIS B 58 PHE 0.044 0.001 PHE A 205 TYR 0.015 0.001 TYR B 457 ARG 0.012 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 601) hydrogen bonds : angle 3.50009 ( 1797) covalent geometry : bond 0.00272 (11132) covalent geometry : angle 0.56658 (15096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8332 (mtt-85) REVERT: A 211 LEU cc_start: 0.9094 (tp) cc_final: 0.8751 (tt) REVERT: A 268 GLU cc_start: 0.7591 (tp30) cc_final: 0.7315 (tp30) REVERT: A 298 CYS cc_start: 0.8136 (m) cc_final: 0.7811 (m) REVERT: A 457 TYR cc_start: 0.5826 (t80) cc_final: 0.5472 (t80) REVERT: A 677 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 693 MET cc_start: 0.7629 (ppp) cc_final: 0.7343 (tmm) REVERT: B 211 LEU cc_start: 0.9130 (tp) cc_final: 0.8801 (tt) REVERT: B 268 GLU cc_start: 0.7654 (tp30) cc_final: 0.7369 (tp30) REVERT: B 298 CYS cc_start: 0.8305 (m) cc_final: 0.8022 (m) REVERT: B 693 MET cc_start: 0.7677 (ppp) cc_final: 0.7414 (tmm) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 0.1808 time to fit residues: 49.6982 Evaluate side-chains 170 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 132 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.084854 restraints weight = 20090.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087544 restraints weight = 10500.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089220 restraints weight = 7187.032| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11132 Z= 0.106 Angle : 0.559 9.737 15096 Z= 0.273 Chirality : 0.039 0.188 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.704 13.936 1444 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 17.42 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1320 helix: 1.30 (0.18), residues: 908 sheet: -0.10 (0.70), residues: 58 loop : -0.92 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 533 HIS 0.003 0.000 HIS B 58 PHE 0.054 0.001 PHE A 205 TYR 0.014 0.001 TYR B 26 ARG 0.004 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 601) hydrogen bonds : angle 3.42068 ( 1797) covalent geometry : bond 0.00240 (11132) covalent geometry : angle 0.55919 (15096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8341 (mtt-85) REVERT: A 211 LEU cc_start: 0.9042 (tp) cc_final: 0.8706 (tt) REVERT: A 268 GLU cc_start: 0.7592 (tp30) cc_final: 0.7321 (tp30) REVERT: A 286 LYS cc_start: 0.7943 (mttt) cc_final: 0.7160 (tttt) REVERT: A 298 CYS cc_start: 0.8120 (m) cc_final: 0.7789 (m) REVERT: A 693 MET cc_start: 0.7606 (ppp) cc_final: 0.7301 (tmm) REVERT: B 211 LEU cc_start: 0.9057 (tp) cc_final: 0.8726 (tt) REVERT: B 268 GLU cc_start: 0.7622 (tp30) cc_final: 0.7344 (tp30) REVERT: B 286 LYS cc_start: 0.7730 (mttt) cc_final: 0.6919 (tttt) REVERT: B 298 CYS cc_start: 0.8290 (m) cc_final: 0.7991 (m) REVERT: B 693 MET cc_start: 0.7738 (ppp) cc_final: 0.7470 (tmm) outliers start: 28 outliers final: 18 residues processed: 190 average time/residue: 0.2444 time to fit residues: 70.1329 Evaluate side-chains 172 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.081833 restraints weight = 20180.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.084403 restraints weight = 10593.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.085998 restraints weight = 7303.916| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11132 Z= 0.187 Angle : 0.624 9.307 15096 Z= 0.310 Chirality : 0.042 0.181 1656 Planarity : 0.004 0.034 1916 Dihedral : 3.823 14.407 1444 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.60 % Allowed : 17.85 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1320 helix: 1.20 (0.18), residues: 910 sheet: -0.19 (0.70), residues: 58 loop : -0.85 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 600 HIS 0.003 0.001 HIS B 58 PHE 0.049 0.002 PHE A 205 TYR 0.016 0.001 TYR B 26 ARG 0.002 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 601) hydrogen bonds : angle 3.64984 ( 1797) covalent geometry : bond 0.00440 (11132) covalent geometry : angle 0.62409 (15096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8360 (mtt-85) REVERT: A 211 LEU cc_start: 0.9110 (tp) cc_final: 0.8800 (tt) REVERT: A 268 GLU cc_start: 0.7667 (tp30) cc_final: 0.7214 (tp30) REVERT: A 298 CYS cc_start: 0.8155 (m) cc_final: 0.7889 (m) REVERT: A 693 MET cc_start: 0.7713 (ppp) cc_final: 0.7313 (tmm) REVERT: B 211 LEU cc_start: 0.9110 (tp) cc_final: 0.8825 (tt) REVERT: B 268 GLU cc_start: 0.7682 (tp30) cc_final: 0.7378 (tp30) REVERT: B 298 CYS cc_start: 0.8295 (m) cc_final: 0.7998 (m) outliers start: 30 outliers final: 25 residues processed: 172 average time/residue: 0.2519 time to fit residues: 66.9508 Evaluate side-chains 169 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 1 optimal weight: 0.0980 chunk 97 optimal weight: 0.1980 chunk 30 optimal weight: 0.0070 chunk 122 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085389 restraints weight = 19874.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088068 restraints weight = 10352.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089740 restraints weight = 7096.030| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11132 Z= 0.107 Angle : 0.581 9.729 15096 Z= 0.285 Chirality : 0.040 0.186 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.724 13.064 1444 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 18.46 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1320 helix: 1.45 (0.18), residues: 908 sheet: -0.11 (0.72), residues: 58 loop : -0.86 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 600 HIS 0.002 0.000 HIS A 58 PHE 0.028 0.001 PHE A 315 TYR 0.014 0.001 TYR B 26 ARG 0.002 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 601) hydrogen bonds : angle 3.46798 ( 1797) covalent geometry : bond 0.00240 (11132) covalent geometry : angle 0.58105 (15096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8296 (mtt-85) REVERT: A 211 LEU cc_start: 0.9079 (tp) cc_final: 0.8759 (tt) REVERT: A 268 GLU cc_start: 0.7612 (tp30) cc_final: 0.7319 (tp30) REVERT: A 286 LYS cc_start: 0.7996 (mttt) cc_final: 0.7200 (tttt) REVERT: A 298 CYS cc_start: 0.8128 (m) cc_final: 0.7807 (m) REVERT: A 693 MET cc_start: 0.7604 (ppp) cc_final: 0.7227 (tmm) REVERT: B 211 LEU cc_start: 0.9080 (tp) cc_final: 0.8786 (tt) REVERT: B 268 GLU cc_start: 0.7636 (tp30) cc_final: 0.7332 (tp30) REVERT: B 286 LYS cc_start: 0.7843 (mttt) cc_final: 0.6977 (tttp) REVERT: B 298 CYS cc_start: 0.8226 (m) cc_final: 0.7959 (m) outliers start: 21 outliers final: 18 residues processed: 172 average time/residue: 0.1823 time to fit residues: 48.2392 Evaluate side-chains 157 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 71 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.084238 restraints weight = 20076.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.086915 restraints weight = 10592.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.088599 restraints weight = 7287.589| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11132 Z= 0.122 Angle : 0.579 9.724 15096 Z= 0.284 Chirality : 0.040 0.175 1656 Planarity : 0.003 0.033 1916 Dihedral : 3.683 13.296 1444 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.08 % Allowed : 18.37 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1320 helix: 1.52 (0.18), residues: 904 sheet: -0.10 (0.72), residues: 58 loop : -0.87 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 533 HIS 0.002 0.001 HIS A 58 PHE 0.052 0.001 PHE B 205 TYR 0.014 0.001 TYR B 26 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 601) hydrogen bonds : angle 3.44626 ( 1797) covalent geometry : bond 0.00283 (11132) covalent geometry : angle 0.57871 (15096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8334 (mtt-85) REVERT: A 205 PHE cc_start: 0.8423 (p90) cc_final: 0.8221 (p90) REVERT: A 211 LEU cc_start: 0.9088 (tp) cc_final: 0.8764 (tt) REVERT: A 268 GLU cc_start: 0.7623 (tp30) cc_final: 0.7341 (tp30) REVERT: A 286 LYS cc_start: 0.7960 (mttt) cc_final: 0.7120 (ttpt) REVERT: A 298 CYS cc_start: 0.8159 (m) cc_final: 0.7817 (m) REVERT: A 693 MET cc_start: 0.7661 (ppp) cc_final: 0.7273 (tmm) REVERT: B 211 LEU cc_start: 0.9100 (tp) cc_final: 0.8783 (tt) REVERT: B 268 GLU cc_start: 0.7629 (tp30) cc_final: 0.7316 (tp30) REVERT: B 286 LYS cc_start: 0.7913 (mttt) cc_final: 0.7045 (tttp) REVERT: B 298 CYS cc_start: 0.8275 (m) cc_final: 0.7989 (m) REVERT: B 693 MET cc_start: 0.7480 (ppp) cc_final: 0.7080 (tmm) outliers start: 24 outliers final: 23 residues processed: 159 average time/residue: 0.1808 time to fit residues: 44.2266 Evaluate side-chains 161 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.0000 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN B 460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.082654 restraints weight = 20001.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085245 restraints weight = 10583.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086861 restraints weight = 7297.088| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11132 Z= 0.157 Angle : 0.605 10.433 15096 Z= 0.299 Chirality : 0.041 0.182 1656 Planarity : 0.004 0.033 1916 Dihedral : 3.743 12.779 1444 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.25 % Allowed : 18.46 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1320 helix: 1.42 (0.18), residues: 910 sheet: -0.13 (0.72), residues: 58 loop : -0.79 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 533 HIS 0.002 0.001 HIS A 58 PHE 0.049 0.001 PHE A 205 TYR 0.016 0.001 TYR B 26 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 601) hydrogen bonds : angle 3.55335 ( 1797) covalent geometry : bond 0.00367 (11132) covalent geometry : angle 0.60491 (15096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8326 (mtt-85) REVERT: A 205 PHE cc_start: 0.8474 (p90) cc_final: 0.8247 (p90) REVERT: A 211 LEU cc_start: 0.9112 (tp) cc_final: 0.8818 (tt) REVERT: A 268 GLU cc_start: 0.7655 (tp30) cc_final: 0.7185 (tp30) REVERT: A 298 CYS cc_start: 0.8144 (m) cc_final: 0.7882 (m) REVERT: A 693 MET cc_start: 0.7701 (ppp) cc_final: 0.7294 (tmm) REVERT: B 195 TYR cc_start: 0.9324 (t80) cc_final: 0.8964 (t80) REVERT: B 211 LEU cc_start: 0.9128 (tp) cc_final: 0.8840 (tt) REVERT: B 268 GLU cc_start: 0.7659 (tp30) cc_final: 0.7346 (tp30) REVERT: B 286 LYS cc_start: 0.7936 (mttt) cc_final: 0.7070 (tttp) REVERT: B 298 CYS cc_start: 0.8313 (m) cc_final: 0.7987 (m) outliers start: 26 outliers final: 22 residues processed: 161 average time/residue: 0.2010 time to fit residues: 49.5605 Evaluate side-chains 156 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 0.0770 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.084573 restraints weight = 19920.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087220 restraints weight = 10484.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.088869 restraints weight = 7198.141| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11132 Z= 0.115 Angle : 0.588 11.603 15096 Z= 0.288 Chirality : 0.040 0.172 1656 Planarity : 0.004 0.032 1916 Dihedral : 3.708 13.043 1444 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.99 % Allowed : 18.98 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1320 helix: 1.53 (0.18), residues: 906 sheet: -0.03 (0.73), residues: 58 loop : -0.85 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 533 HIS 0.002 0.000 HIS A 58 PHE 0.050 0.001 PHE B 205 TYR 0.015 0.001 TYR B 26 ARG 0.008 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 601) hydrogen bonds : angle 3.45799 ( 1797) covalent geometry : bond 0.00264 (11132) covalent geometry : angle 0.58834 (15096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.92 seconds wall clock time: 66 minutes 27.62 seconds (3987.62 seconds total)