Starting phenix.real_space_refine on Sat Jul 4 00:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpx_41496/07_2026/8tpx_41496.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 10672 2.51 5 N 3124 2.21 5 O 3331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17177 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6719 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 895, 6675 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 848} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 895, 6675 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 848} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 6753 Chain: "B" Number of atoms: 6763 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 901, 6711 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 855} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 901, 6711 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 855} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 6779 Chain: "C" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG A 13 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG A 13 " occ=0.56 residue: pdb=" N AARG A 27 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG A 27 " occ=0.52 residue: pdb=" N AARG A 486 " occ=0.47 ... (20 atoms not shown) pdb=" NH2BARG A 486 " occ=0.53 residue: pdb=" N AARG B 13 " occ=0.34 ... (20 atoms not shown) pdb=" NH2BARG B 13 " occ=0.66 residue: pdb=" N AARG B 27 " occ=0.86 ... (20 atoms not shown) pdb=" NH2BARG B 27 " occ=0.14 residue: pdb=" N AARG B 58 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.57 Time building chain proxies: 4.60, per 1000 atoms: 0.27 Number of scatterers: 17177 At special positions: 0 Unit cell: (96.8, 117.7, 192.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 3331 8.00 N 3124 7.00 C 10672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 39 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 34.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 4.274A pdb=" N VAL A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 4.392A pdb=" N GLU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.551A pdb=" N ALA A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.706A pdb=" N ARG A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.730A pdb=" N ARG A 144 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 191 removed outlier: 3.749A pdb=" N TYR A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 220 Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.763A pdb=" N SER A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.063A pdb=" N VAL A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 removed outlier: 3.503A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.511A pdb=" N LEU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.741A pdb=" N LEU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.831A pdb=" N ARG A 514 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA A 515 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.729A pdb=" N GLU A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 582 through 597 removed outlier: 3.577A pdb=" N ALA A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 610 Processing helix chain 'A' and resid 619 through 640 Proline residue: A 625 - end of helix removed outlier: 4.008A pdb=" N SER A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 654 through 662 Processing helix chain 'A' and resid 666 through 683 removed outlier: 3.793A pdb=" N SER A 683 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 729 through 741 removed outlier: 3.665A pdb=" N GLU A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.007A pdb=" N LEU A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 811 through 820 removed outlier: 3.509A pdb=" N GLU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.730A pdb=" N VAL A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 31 Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.652A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.530A pdb=" N ALA B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 removed outlier: 3.745A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 181 through 191 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.679A pdb=" N GLN B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.780A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.834A pdb=" N GLY B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 497 removed outlier: 3.606A pdb=" N AARG B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 514 removed outlier: 4.272A pdb=" N ARG B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 540 Processing helix chain 'B' and resid 577 through 582 Processing helix chain 'B' and resid 582 through 597 removed outlier: 3.576A pdb=" N ALA B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 603 through 610 removed outlier: 3.713A pdb=" N VAL B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 640 removed outlier: 3.579A pdb=" N GLN B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Proline residue: B 625 - end of helix Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.883A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 697 through 704 Processing helix chain 'B' and resid 727 through 739 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.511A pdb=" N VAL B 762 " --> pdb=" O ILE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 771 removed outlier: 3.904A pdb=" N LEU B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 769 " --> pdb=" O GLU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 810 through 822 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 864 through 878 removed outlier: 3.686A pdb=" N PHE B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.822A pdb=" N VAL B 886 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 1415 through 1429 removed outlier: 4.362A pdb=" N LEU C1419 " --> pdb=" O ASN C1415 " (cutoff:3.500A) Processing helix chain 'C' and resid 1441 through 1446 Processing helix chain 'C' and resid 1450 through 1463 Processing helix chain 'C' and resid 1470 through 1475 Processing helix chain 'C' and resid 1477 through 1481 Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.839A pdb=" N ASP H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 182 removed outlier: 3.573A pdb=" N LEU H 182 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 150 removed outlier: 3.548A pdb=" N LEU L 147 " --> pdb=" O SER L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.295A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY A 228 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 230 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 38 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A 276 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 36 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 293 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 441 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 removed outlier: 4.337A pdb=" N GLN A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.643A pdb=" N VAL A 473 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 525 " --> pdb=" O VAL A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 692 Processing sheet with id=AA6, first strand: chain 'B' and resid 196 through 199 removed outlier: 3.969A pdb=" N GLY B 153 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 230 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 270 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 41 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 272 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET B 39 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 274 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 37 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 293 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG B 437 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 334 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 477 Processing sheet with id=AA8, first strand: chain 'B' and resid 781 through 782 removed outlier: 6.792A pdb=" N VAL B 560 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL B 649 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 562 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 689 through 693 removed outlier: 3.516A pdb=" N GLY B 689 " --> pdb=" O GLY B 726 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 726 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 722 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 715 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.862A pdb=" N LEU H 22 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AB3, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=AB4, first strand: chain 'L' and resid 27 through 29 removed outlier: 3.672A pdb=" N LEU L 27 " --> pdb=" O LYS L 125 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP L 127 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE L 69 " --> pdb=" O TRP L 56 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU L 58 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU L 67 " --> pdb=" O LEU L 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'L' and resid 138 through 140 removed outlier: 3.543A pdb=" N LEU L 157 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE L 140 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL L 155 " --> pdb=" O PHE L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 216 through 218 589 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3329 1.32 - 1.45: 4237 1.45 - 1.57: 9866 1.57 - 1.69: 2 1.69 - 1.81: 79 Bond restraints: 17513 Sorted by residual: bond pdb=" N ASN B 351 " pdb=" CA ASN B 351 " ideal model delta sigma weight residual 1.458 1.501 -0.044 1.42e-02 4.96e+03 9.41e+00 bond pdb=" CT 4HH C1449 " pdb=" SU 4HH C1449 " ideal model delta sigma weight residual 1.825 1.772 0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C PRO A 50 " pdb=" O PRO A 50 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" CL3 4HH C1449 " pdb=" NN 4HH C1449 " ideal model delta sigma weight residual 1.335 1.385 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" N ASP B 355 " pdb=" CA ASP B 355 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.33e-02 5.65e+03 5.54e+00 ... (remaining 17508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 23476 2.58 - 5.15: 301 5.15 - 7.73: 29 7.73 - 10.31: 5 10.31 - 12.88: 5 Bond angle restraints: 23816 Sorted by residual: angle pdb=" N LEU B 353 " pdb=" CA LEU B 353 " pdb=" C LEU B 353 " ideal model delta sigma weight residual 113.18 101.30 11.88 1.21e+00 6.83e-01 9.64e+01 angle pdb=" N ASP B 355 " pdb=" CA ASP B 355 " pdb=" C ASP B 355 " ideal model delta sigma weight residual 113.28 101.67 11.61 1.22e+00 6.72e-01 9.06e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 113.28 102.35 10.93 1.22e+00 6.72e-01 8.03e+01 angle pdb=" C TYR B 159 " pdb=" CA TYR B 159 " pdb=" CB TYR B 159 " ideal model delta sigma weight residual 116.63 110.86 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C VAL A 47 " pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta sigma weight residual 122.11 114.87 7.24 1.59e+00 3.96e-01 2.08e+01 ... (remaining 23811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9341 17.95 - 35.89: 879 35.89 - 53.84: 236 53.84 - 71.78: 42 71.78 - 89.73: 16 Dihedral angle restraints: 10514 sinusoidal: 4043 harmonic: 6471 Sorted by residual: dihedral pdb=" CB CYS L 39 " pdb=" SG CYS L 39 " pdb=" SG CYS L 109 " pdb=" CB CYS L 109 " ideal model delta sinusoidal sigma weight residual 93.00 155.49 -62.49 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CA THR B 410 " pdb=" C THR B 410 " pdb=" N PRO B 411 " pdb=" CA PRO B 411 " ideal model delta harmonic sigma weight residual 180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASP B 74 " pdb=" C ASP B 74 " pdb=" N LEU B 75 " pdb=" CA LEU B 75 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 10511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2307 0.060 - 0.119: 344 0.119 - 0.178: 26 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA LEU B 354 " pdb=" N LEU B 354 " pdb=" C LEU B 354 " pdb=" CB LEU B 354 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2677 not shown) Planarity restraints: 3172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 46 " -0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C GLY A 46 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY A 46 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL A 47 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 355 " 0.024 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C ASP B 355 " -0.086 2.00e-02 2.50e+03 pdb=" O ASP B 355 " 0.032 2.00e-02 2.50e+03 pdb=" N THR B 356 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 354 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C LEU B 354 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU B 354 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 355 " -0.019 2.00e-02 2.50e+03 ... (remaining 3169 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2536 2.75 - 3.29: 18103 3.29 - 3.83: 28225 3.83 - 4.36: 31250 4.36 - 4.90: 52990 Nonbonded interactions: 133104 Sorted by model distance: nonbonded pdb=" OG1 THR H 73 " pdb=" OD1 ASN H 88 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 666 " pdb=" OE1 GLU B 668 " model vdw 2.222 3.040 nonbonded pdb=" O LEU A 637 " pdb=" OG SER A 640 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 90 " pdb=" O LEU A 248 " model vdw 2.231 3.040 nonbonded pdb=" N GLU C1431 " pdb=" OE1 GLU C1431 " model vdw 2.233 3.120 ... (remaining 133099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 95 or (resid 96 and (name N or name \ CA or name C or name O or name CB )) or resid 97 through 485 or resid 487 throug \ h 908)) selection = (chain 'B' and (resid 3 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 162 or resid 171 through 485 or resi \ d 487 through 595 or (resid 596 through 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 908)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.600 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.680 Find NCS groups from input model: 0.200 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.003 0.053 17517 Z= 0.164 Angle : 0.696 12.883 23824 Z= 0.377 Chirality : 0.042 0.297 2680 Planarity : 0.005 0.075 3172 Dihedral : 15.365 89.726 6362 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.76 % Allowed : 14.08 % Favored : 85.16 % Rotamer: Outliers : 0.73 % Allowed : 17.01 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 2278 helix: 1.43 (0.21), residues: 681 sheet: -0.55 (0.33), residues: 281 loop : -2.42 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 359 TYR 0.019 0.001 TYR A 906 PHE 0.011 0.001 PHE B 157 TRP 0.015 0.001 TRP A 54 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (17513) covalent geometry : angle 0.69630 / 0.38 (23816) SS BOND : bond 0.00202 / 0.10 ( 4) SS BOND : angle 0.69614 / 0.40 ( 8) hydrogen bonds : bond 0.16714 / 11.43 ( 589) hydrogen bonds : angle 6.45322 / 4.52 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.1306 time to fit residues: 16.1237 Evaluate side-chains 69 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain B residue 585 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.2980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035005 restraints weight = 447400.867| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 10.77 r_work: 0.2663 rms_B_bonded: 9.92 restraints_weight: 2.0000 r_work: 0.2784 rms_B_bonded: 6.44 restraints_weight: 4.0000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17517 Z= 0.130 Angle : 0.652 13.827 23824 Z= 0.332 Chirality : 0.042 0.224 2680 Planarity : 0.005 0.077 3172 Dihedral : 6.192 59.171 2551 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.37 % Favored : 86.05 % Rotamer: Outliers : 1.86 % Allowed : 16.06 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 2278 helix: 1.65 (0.21), residues: 700 sheet: -0.96 (0.31), residues: 307 loop : -2.50 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1439 TYR 0.020 0.001 TYR A 906 PHE 0.019 0.001 PHE B 157 TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (17513) covalent geometry : angle 0.65251 / 0.33 (23816) SS BOND : bond 0.00183 / 0.08 ( 4) SS BOND : angle 0.60190 / 0.33 ( 8) hydrogen bonds : bond 0.03908 / 2.67 ( 589) hydrogen bonds : angle 4.58723 / 3.24 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 599 MET cc_start: 0.9358 (tmm) cc_final: 0.9006 (tmm) REVERT: A 791 MET cc_start: 0.8375 (mmm) cc_final: 0.7495 (mmm) REVERT: C 1444 GLU cc_start: 0.4611 (tp30) cc_final: 0.4337 (tp30) REVERT: H 129 PHE cc_start: 0.8403 (t80) cc_final: 0.7320 (t80) REVERT: L 155 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8346 (t) outliers start: 29 outliers final: 12 residues processed: 98 average time/residue: 0.1289 time to fit residues: 19.6153 Evaluate side-chains 84 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 585 PHE Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain L residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 197 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 121 optimal weight: 0.3980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033632 restraints weight = 506049.117| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 11.60 r_work: 0.2596 rms_B_bonded: 10.26 restraints_weight: 2.0000 r_work: 0.2721 rms_B_bonded: 6.59 restraints_weight: 4.0000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17517 Z= 0.166 Angle : 0.669 14.549 23824 Z= 0.341 Chirality : 0.042 0.150 2680 Planarity : 0.005 0.079 3172 Dihedral : 6.016 58.881 2547 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.58 % Allowed : 14.22 % Favored : 85.21 % Rotamer: Outliers : 2.03 % Allowed : 15.83 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2278 helix: 1.72 (0.21), residues: 699 sheet: -1.08 (0.31), residues: 310 loop : -2.53 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 817 TYR 0.020 0.001 TYR A 906 PHE 0.016 0.001 PHE C1442 TRP 0.010 0.001 TRP A 801 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17513) covalent geometry : angle 0.66930 / 0.34 (23816) SS BOND : bond 0.00256 / 0.12 ( 4) SS BOND : angle 0.57911 / 0.33 ( 8) hydrogen bonds : bond 0.04062 / 2.75 ( 589) hydrogen bonds : angle 4.46518 / 3.15 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.9337 (tpp) cc_final: 0.9047 (ttm) REVERT: A 599 MET cc_start: 0.9399 (tmm) cc_final: 0.9012 (tmm) REVERT: A 681 MET cc_start: 0.9624 (tmm) cc_final: 0.9316 (tmm) REVERT: C 1439 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8762 (mtm110) outliers start: 33 outliers final: 20 residues processed: 100 average time/residue: 0.1242 time to fit residues: 19.1702 Evaluate side-chains 88 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 585 PHE Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 117 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 140 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.050597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034335 restraints weight = 472694.667| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 11.60 r_work: 0.2624 rms_B_bonded: 10.25 restraints_weight: 2.0000 r_work: 0.2748 rms_B_bonded: 6.59 restraints_weight: 4.0000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17517 Z= 0.125 Angle : 0.646 15.572 23824 Z= 0.328 Chirality : 0.042 0.173 2680 Planarity : 0.004 0.077 3172 Dihedral : 5.867 57.346 2547 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.11 % Favored : 86.27 % Rotamer: Outliers : 2.14 % Allowed : 16.11 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 2278 helix: 1.77 (0.21), residues: 694 sheet: -1.01 (0.31), residues: 315 loop : -2.50 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 480 TYR 0.025 0.001 TYR B 802 PHE 0.014 0.001 PHE B 157 TRP 0.010 0.001 TRP A 54 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17513) covalent geometry : angle 0.64564 / 0.33 (23816) SS BOND : bond 0.00209 / 0.10 ( 4) SS BOND : angle 0.51645 / 0.28 ( 8) hydrogen bonds : bond 0.03437 / 2.31 ( 589) hydrogen bonds : angle 4.28724 / 3.04 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.666 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 118 MET cc_start: 0.8984 (ttt) cc_final: 0.8660 (ttt) REVERT: A 599 MET cc_start: 0.9324 (tmm) cc_final: 0.9034 (tmm) REVERT: A 681 MET cc_start: 0.9633 (tmm) cc_final: 0.9303 (tmm) REVERT: C 1439 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8676 (mtm110) REVERT: H 129 PHE cc_start: 0.8295 (t80) cc_final: 0.7733 (t80) REVERT: H 173 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4994 (t80) outliers start: 35 outliers final: 25 residues processed: 103 average time/residue: 0.1333 time to fit residues: 21.3694 Evaluate side-chains 97 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 221 optimal weight: 0.4980 chunk 213 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.034240 restraints weight = 444101.454| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 10.60 r_work: 0.2645 rms_B_bonded: 9.69 restraints_weight: 2.0000 r_work: 0.2765 rms_B_bonded: 6.30 restraints_weight: 4.0000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17517 Z= 0.124 Angle : 0.643 14.570 23824 Z= 0.323 Chirality : 0.042 0.209 2680 Planarity : 0.004 0.074 3172 Dihedral : 5.608 53.917 2545 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.51 % Favored : 85.92 % Rotamer: Outliers : 2.25 % Allowed : 16.45 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2278 helix: 1.80 (0.21), residues: 697 sheet: -1.03 (0.31), residues: 318 loop : -2.50 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 436 TYR 0.021 0.001 TYR A 906 PHE 0.011 0.001 PHE B 157 TRP 0.008 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17513) covalent geometry : angle 0.64289 / 0.32 (23816) SS BOND : bond 0.00221 / 0.10 ( 4) SS BOND : angle 0.52485 / 0.29 ( 8) hydrogen bonds : bond 0.03323 / 2.23 ( 589) hydrogen bonds : angle 4.19091 / 2.97 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8968 (ttt) cc_final: 0.8700 (ttt) REVERT: A 233 MET cc_start: 0.9345 (tpp) cc_final: 0.9062 (ttm) REVERT: A 535 LEU cc_start: 0.9345 (tt) cc_final: 0.8815 (pp) REVERT: A 599 MET cc_start: 0.9330 (tmm) cc_final: 0.9032 (tmm) REVERT: A 681 MET cc_start: 0.9637 (tmm) cc_final: 0.9327 (tmm) REVERT: C 1444 GLU cc_start: 0.4740 (tp30) cc_final: 0.4465 (tp30) REVERT: H 21 ARG cc_start: 0.9064 (tpt170) cc_final: 0.8629 (tpt170) REVERT: H 173 PHE cc_start: 0.5942 (OUTLIER) cc_final: 0.4902 (t80) REVERT: L 110 MET cc_start: 0.9145 (mmm) cc_final: 0.8735 (mmm) outliers start: 37 outliers final: 25 residues processed: 105 average time/residue: 0.1299 time to fit residues: 20.8922 Evaluate side-chains 97 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 25 optimal weight: 0.0970 chunk 131 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.050832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.034466 restraints weight = 445606.755| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 10.71 r_work: 0.2656 rms_B_bonded: 9.97 restraints_weight: 2.0000 r_work: 0.2777 rms_B_bonded: 6.44 restraints_weight: 4.0000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17517 Z= 0.116 Angle : 0.648 16.049 23824 Z= 0.323 Chirality : 0.042 0.250 2680 Planarity : 0.004 0.072 3172 Dihedral : 5.508 53.243 2545 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.53 % Favored : 86.94 % Rotamer: Outliers : 2.14 % Allowed : 16.96 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 2278 helix: 1.84 (0.21), residues: 697 sheet: -0.94 (0.32), residues: 304 loop : -2.51 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 76 TYR 0.021 0.001 TYR A 906 PHE 0.030 0.001 PHE H 129 TRP 0.007 0.001 TRP A 54 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17513) covalent geometry : angle 0.64762 / 0.32 (23816) SS BOND : bond 0.00215 / 0.10 ( 4) SS BOND : angle 0.54965 / 0.29 ( 8) hydrogen bonds : bond 0.03158 / 2.12 ( 589) hydrogen bonds : angle 4.11545 / 2.92 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8934 (ttt) cc_final: 0.8659 (ttt) REVERT: A 233 MET cc_start: 0.9353 (tpp) cc_final: 0.9061 (ttm) REVERT: A 535 LEU cc_start: 0.9309 (tt) cc_final: 0.8796 (pp) REVERT: A 599 MET cc_start: 0.9355 (tmm) cc_final: 0.9054 (tmm) REVERT: A 681 MET cc_start: 0.9643 (tmm) cc_final: 0.9318 (tmm) REVERT: B 246 ARG cc_start: 0.8789 (ttt90) cc_final: 0.8573 (ttt-90) REVERT: C 1444 GLU cc_start: 0.4648 (tp30) cc_final: 0.4367 (tp30) REVERT: C 1475 HIS cc_start: 0.3788 (p90) cc_final: 0.3575 (p-80) REVERT: H 21 ARG cc_start: 0.9020 (tpt170) cc_final: 0.8604 (tpt170) REVERT: H 173 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4944 (t80) outliers start: 35 outliers final: 29 residues processed: 104 average time/residue: 0.1281 time to fit residues: 20.2127 Evaluate side-chains 101 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 137 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.050751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034533 restraints weight = 424207.393| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 10.36 r_work: 0.2658 rms_B_bonded: 9.79 restraints_weight: 2.0000 r_work: 0.2780 rms_B_bonded: 6.31 restraints_weight: 4.0000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17517 Z= 0.119 Angle : 0.653 16.061 23824 Z= 0.325 Chirality : 0.042 0.184 2680 Planarity : 0.004 0.071 3172 Dihedral : 5.470 54.128 2545 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.06 % Favored : 86.41 % Rotamer: Outliers : 2.14 % Allowed : 17.07 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 2278 helix: 1.84 (0.21), residues: 698 sheet: -0.92 (0.32), residues: 304 loop : -2.49 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 732 TYR 0.021 0.001 TYR A 906 PHE 0.010 0.001 PHE B 157 TRP 0.007 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (17513) covalent geometry : angle 0.65262 / 0.32 (23816) SS BOND : bond 0.00202 / 0.09 ( 4) SS BOND : angle 0.52494 / 0.28 ( 8) hydrogen bonds : bond 0.03154 / 2.13 ( 589) hydrogen bonds : angle 4.09030 / 2.90 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8924 (ttt) cc_final: 0.8658 (ttt) REVERT: A 233 MET cc_start: 0.9351 (tpp) cc_final: 0.9064 (ttm) REVERT: A 535 LEU cc_start: 0.9306 (tt) cc_final: 0.8776 (pp) REVERT: A 681 MET cc_start: 0.9650 (tmm) cc_final: 0.9321 (tmm) REVERT: C 1444 GLU cc_start: 0.4671 (tp30) cc_final: 0.4381 (tp30) REVERT: C 1475 HIS cc_start: 0.3888 (p90) cc_final: 0.3662 (p-80) REVERT: H 21 ARG cc_start: 0.9005 (tpt170) cc_final: 0.8587 (tpt170) REVERT: H 173 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.4960 (t80) REVERT: L 110 MET cc_start: 0.9104 (mmm) cc_final: 0.8720 (mmm) outliers start: 35 outliers final: 32 residues processed: 104 average time/residue: 0.1277 time to fit residues: 20.3763 Evaluate side-chains 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.0570 chunk 61 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 8 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.034950 restraints weight = 450212.434| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 10.89 r_work: 0.2674 rms_B_bonded: 10.03 restraints_weight: 2.0000 r_work: 0.2798 rms_B_bonded: 6.49 restraints_weight: 4.0000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17517 Z= 0.109 Angle : 0.643 15.600 23824 Z= 0.321 Chirality : 0.042 0.173 2680 Planarity : 0.004 0.070 3172 Dihedral : 5.338 53.480 2545 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.66 % Favored : 86.81 % Rotamer: Outliers : 2.14 % Allowed : 17.24 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 2278 helix: 2.01 (0.21), residues: 684 sheet: -1.00 (0.31), residues: 321 loop : -2.49 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1439 TYR 0.022 0.001 TYR A 906 PHE 0.032 0.001 PHE H 129 TRP 0.007 0.001 TRP A 429 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17513) covalent geometry : angle 0.64309 / 0.32 (23816) SS BOND : bond 0.00204 / 0.09 ( 4) SS BOND : angle 0.57954 / 0.31 ( 8) hydrogen bonds : bond 0.02912 / 1.96 ( 589) hydrogen bonds : angle 4.02023 / 2.86 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8892 (ttt) cc_final: 0.8612 (ttt) REVERT: A 535 LEU cc_start: 0.9289 (tt) cc_final: 0.8773 (pp) REVERT: A 599 MET cc_start: 0.9254 (tmm) cc_final: 0.8925 (tmm) REVERT: A 681 MET cc_start: 0.9659 (tmm) cc_final: 0.9308 (tmm) REVERT: B 246 ARG cc_start: 0.8920 (ttt-90) cc_final: 0.8592 (ttt90) REVERT: C 1444 GLU cc_start: 0.4730 (tp30) cc_final: 0.4464 (tp30) REVERT: C 1475 HIS cc_start: 0.3952 (p90) cc_final: 0.3714 (p-80) REVERT: H 21 ARG cc_start: 0.9021 (tpt170) cc_final: 0.8392 (tpp-160) REVERT: H 38 TRP cc_start: 0.6548 (OUTLIER) cc_final: 0.6345 (t-100) REVERT: H 173 PHE cc_start: 0.5926 (OUTLIER) cc_final: 0.4797 (t80) outliers start: 36 outliers final: 33 residues processed: 106 average time/residue: 0.1241 time to fit residues: 20.2754 Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 46 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034666 restraints weight = 472917.821| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 11.02 r_work: 0.2661 rms_B_bonded: 10.18 restraints_weight: 2.0000 r_work: 0.2784 rms_B_bonded: 6.60 restraints_weight: 4.0000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17517 Z= 0.114 Angle : 0.644 15.379 23824 Z= 0.320 Chirality : 0.042 0.190 2680 Planarity : 0.004 0.070 3172 Dihedral : 5.315 53.854 2545 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.88 % Favored : 86.58 % Rotamer: Outliers : 2.14 % Allowed : 17.30 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 2278 helix: 1.99 (0.21), residues: 691 sheet: -1.01 (0.31), residues: 314 loop : -2.47 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1439 TYR 0.021 0.001 TYR A 906 PHE 0.009 0.001 PHE B 157 TRP 0.007 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17513) covalent geometry : angle 0.64370 / 0.32 (23816) SS BOND : bond 0.00229 / 0.10 ( 4) SS BOND : angle 0.53965 / 0.29 ( 8) hydrogen bonds : bond 0.02996 / 2.02 ( 589) hydrogen bonds : angle 3.99831 / 2.84 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.495 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 118 MET cc_start: 0.8881 (ttt) cc_final: 0.8621 (ttt) REVERT: A 535 LEU cc_start: 0.9273 (tt) cc_final: 0.8747 (pp) REVERT: A 599 MET cc_start: 0.9183 (tmm) cc_final: 0.8864 (tmm) REVERT: A 681 MET cc_start: 0.9655 (tmm) cc_final: 0.9302 (tmm) REVERT: A 791 MET cc_start: 0.8163 (mmm) cc_final: 0.7161 (mmm) REVERT: C 1444 GLU cc_start: 0.4704 (tp30) cc_final: 0.4409 (tp30) REVERT: H 21 ARG cc_start: 0.9042 (tpt170) cc_final: 0.8417 (tpp-160) REVERT: H 38 TRP cc_start: 0.6657 (OUTLIER) cc_final: 0.6434 (t-100) REVERT: H 173 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.4837 (t80) outliers start: 36 outliers final: 33 residues processed: 105 average time/residue: 0.1179 time to fit residues: 19.3438 Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 185 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 146 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 223 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 123 optimal weight: 0.0570 chunk 151 optimal weight: 3.9990 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1483 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.052124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035861 restraints weight = 435459.056| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 10.86 r_work: 0.2710 rms_B_bonded: 10.14 restraints_weight: 2.0000 r_work: 0.2837 rms_B_bonded: 6.51 restraints_weight: 4.0000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17517 Z= 0.106 Angle : 0.642 14.688 23824 Z= 0.318 Chirality : 0.041 0.164 2680 Planarity : 0.004 0.068 3172 Dihedral : 5.133 53.765 2545 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.22 % Favored : 87.25 % Rotamer: Outliers : 1.86 % Allowed : 17.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 2278 helix: 2.11 (0.21), residues: 676 sheet: -0.82 (0.32), residues: 305 loop : -2.46 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1439 TYR 0.021 0.001 TYR A 906 PHE 0.032 0.001 PHE H 129 TRP 0.011 0.001 TRP A 429 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (17513) covalent geometry : angle 0.64171 / 0.32 (23816) SS BOND : bond 0.00226 / 0.09 ( 4) SS BOND : angle 0.55411 / 0.29 ( 8) hydrogen bonds : bond 0.02663 / 1.78 ( 589) hydrogen bonds : angle 3.93412 / 2.80 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8830 (ttt) cc_final: 0.8555 (ttt) REVERT: A 535 LEU cc_start: 0.9231 (tt) cc_final: 0.8725 (pp) REVERT: A 681 MET cc_start: 0.9659 (tmm) cc_final: 0.9295 (tmm) REVERT: A 791 MET cc_start: 0.8150 (mmm) cc_final: 0.7159 (mmm) REVERT: C 1444 GLU cc_start: 0.4593 (tp30) cc_final: 0.4320 (tp30) REVERT: H 173 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.4761 (t80) REVERT: L 110 MET cc_start: 0.8950 (mmm) cc_final: 0.8594 (mmm) REVERT: L 177 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8531 (pp30) outliers start: 31 outliers final: 26 residues processed: 102 average time/residue: 0.1214 time to fit residues: 19.1907 Evaluate side-chains 100 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 84 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 171 optimal weight: 0.3980 chunk 127 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.035118 restraints weight = 461283.152| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 11.55 r_work: 0.2658 rms_B_bonded: 10.25 restraints_weight: 2.0000 r_work: 0.2783 rms_B_bonded: 6.54 restraints_weight: 4.0000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17517 Z= 0.117 Angle : 0.644 14.932 23824 Z= 0.320 Chirality : 0.042 0.199 2680 Planarity : 0.004 0.070 3172 Dihedral : 5.064 48.308 2545 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.84 % Favored : 86.72 % Rotamer: Outliers : 1.86 % Allowed : 17.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 2278 helix: 2.12 (0.21), residues: 684 sheet: -0.85 (0.32), residues: 305 loop : -2.48 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1439 TYR 0.021 0.001 TYR A 906 PHE 0.008 0.001 PHE A 264 TRP 0.008 0.001 TRP H 38 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17513) covalent geometry : angle 0.64432 / 0.32 (23816) SS BOND : bond 0.00248 / 0.11 ( 4) SS BOND : angle 0.56143 / 0.31 ( 8) hydrogen bonds : bond 0.02947 / 1.99 ( 589) hydrogen bonds : angle 3.93619 / 2.80 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5853.43 seconds wall clock time: 100 minutes 13.66 seconds (6013.66 seconds total)