Starting phenix.real_space_refine on Sun Aug 24 05:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpx_41496/08_2025/8tpx_41496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpx_41496/08_2025/8tpx_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_41496/08_2025/8tpx_41496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpx_41496/08_2025/8tpx_41496.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpx_41496/08_2025/8tpx_41496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpx_41496/08_2025/8tpx_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 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: 7.10, per 1000 atoms: 0.41 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: 1.57 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.67 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: 3.30 Time building geometry restraints manager: 2.10 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=" 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=" 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 bond pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.43e+00 bond pdb=" CA ALA B 352 " pdb=" CB ALA B 352 " ideal model delta sigma weight residual 1.531 1.494 0.037 1.59e-02 3.96e+03 5.33e+00 ... (remaining 17508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 23486 2.58 - 5.15: 291 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: 9330 17.95 - 35.89: 877 35.89 - 53.84: 233 53.84 - 71.78: 35 71.78 - 89.73: 15 Dihedral angle restraints: 10490 sinusoidal: 4019 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 10487 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: 12.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.630 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 0.044 17517 Z= 0.158 Angle : 0.692 12.883 23824 Z= 0.376 Chirality : 0.042 0.297 2680 Planarity : 0.005 0.075 3172 Dihedral : 15.184 89.726 6338 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 aren 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 covalent geometry : bond 0.00321 (17513) covalent geometry : angle 0.69165 (23816) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.69614 ( 8) hydrogen bonds : bond 0.16714 ( 589) hydrogen bonds : angle 6.45322 ( 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 : 0.621 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: 0.1823 time to fit residues: 22.1231 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 : 0.686 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3456 r_free = 0.3456 target = 0.051144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035032 restraints weight = 447741.426| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 10.82 r_work: 0.2661 rms_B_bonded: 9.90 restraints_weight: 2.0000 r_work: 0.2785 rms_B_bonded: 6.31 restraints_weight: 4.0000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17517 Z= 0.130 Angle : 0.650 13.802 23824 Z= 0.331 Chirality : 0.042 0.239 2680 Planarity : 0.005 0.079 3172 Dihedral : 5.159 57.876 2527 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.28 % Favored : 86.14 % Rotamer: Outliers : 1.86 % Allowed : 16.00 % 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 aren not related in a simple way. whole: -1.31 (0.18), residues: 2278 helix: 1.66 (0.21), residues: 700 sheet: -0.88 (0.32), residues: 295 loop : -2.50 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1439 TYR 0.020 0.001 TYR A 906 PHE 0.026 0.001 PHE C1442 TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00285 (17513) covalent geometry : angle 0.64965 (23816) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.57708 ( 8) hydrogen bonds : bond 0.03979 ( 589) hydrogen bonds : angle 4.59293 ( 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 : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.9347 (tmm) cc_final: 0.8995 (tmm) REVERT: A 791 MET cc_start: 0.8395 (mmm) cc_final: 0.7518 (mmm) REVERT: C 1444 GLU cc_start: 0.4644 (tp30) cc_final: 0.4372 (tp30) REVERT: H 129 PHE cc_start: 0.8420 (t80) cc_final: 0.7346 (t80) REVERT: L 155 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8329 (t) outliers start: 29 outliers final: 13 residues processed: 98 average time/residue: 0.1566 time to fit residues: 23.4412 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 : 0.676 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 121 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.034560 restraints weight = 505492.671| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 11.74 r_work: 0.2642 rms_B_bonded: 10.27 restraints_weight: 2.0000 r_work: 0.2769 rms_B_bonded: 6.52 restraints_weight: 4.0000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 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 = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17517 Z= 0.126 Angle : 0.637 13.865 23824 Z= 0.323 Chirality : 0.042 0.204 2680 Planarity : 0.004 0.077 3172 Dihedral : 5.078 57.450 2523 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.46 % Favored : 85.96 % 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 aren not related in a simple way. whole: -1.31 (0.18), residues: 2278 helix: 1.72 (0.21), residues: 701 sheet: -0.99 (0.31), residues: 307 loop : -2.52 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1439 TYR 0.021 0.001 TYR A 906 PHE 0.015 0.001 PHE B 157 TRP 0.008 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00281 (17513) covalent geometry : angle 0.63729 (23816) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.50506 ( 8) hydrogen bonds : bond 0.03572 ( 589) hydrogen bonds : angle 4.36941 ( 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 101 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.9350 (tmm) cc_final: 0.8961 (tmm) REVERT: C 1439 ARG cc_start: 0.8948 (mtm110) cc_final: 0.8722 (mtm110) REVERT: C 1444 GLU cc_start: 0.4769 (tp30) cc_final: 0.4404 (tp30) REVERT: H 129 PHE cc_start: 0.8325 (t80) cc_final: 0.7349 (t80) REVERT: L 155 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8351 (t) outliers start: 29 outliers final: 20 residues processed: 97 average time/residue: 0.1550 time to fit residues: 22.9245 Evaluate side-chains 93 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 506 VAL Chi-restraints excluded: chain A residue 549 VAL 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 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 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 L residue 106 VAL Chi-restraints excluded: chain L residue 155 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: 0.9990 chunk 206 optimal weight: 0.6980 chunk 203 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.0170 chunk 140 optimal weight: 5.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3454 r_free = 0.3454 target = 0.051060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034798 restraints weight = 473813.940| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 11.60 r_work: 0.2647 rms_B_bonded: 10.26 restraints_weight: 2.0000 r_work: 0.2775 rms_B_bonded: 6.50 restraints_weight: 4.0000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1219 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= 0.119 Angle : 0.632 15.681 23824 Z= 0.320 Chirality : 0.042 0.149 2680 Planarity : 0.004 0.075 3172 Dihedral : 5.087 59.865 2523 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.19 % Favored : 86.23 % Rotamer: Outliers : 1.92 % Allowed : 15.94 % 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 aren not related in a simple way. whole: -1.29 (0.18), residues: 2278 helix: 1.76 (0.21), residues: 701 sheet: -0.98 (0.31), residues: 307 loop : -2.52 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.030 0.001 TYR B 802 PHE 0.013 0.001 PHE B 157 TRP 0.009 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00264 (17513) covalent geometry : angle 0.63249 (23816) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.50894 ( 8) hydrogen bonds : bond 0.03252 ( 589) hydrogen bonds : angle 4.24761 ( 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 105 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.715 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 599 MET cc_start: 0.9292 (tmm) cc_final: 0.9024 (tmm) REVERT: A 681 MET cc_start: 0.9610 (tmm) cc_final: 0.9304 (tmm) REVERT: C 1439 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8675 (mtm110) REVERT: C 1444 GLU cc_start: 0.4819 (tp30) cc_final: 0.4570 (tp30) REVERT: H 129 PHE cc_start: 0.8290 (t80) cc_final: 0.7657 (t80) REVERT: L 155 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8463 (t) outliers start: 31 outliers final: 20 residues processed: 102 average time/residue: 0.1563 time to fit residues: 24.2173 Evaluate side-chains 94 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 388 LEU 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 214 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 155 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: 3.9990 chunk 213 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 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 = 0.3452 r_free = 0.3452 target = 0.051002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034656 restraints weight = 443103.484| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 10.73 r_work: 0.2666 rms_B_bonded: 10.17 restraints_weight: 2.0000 r_work: 0.2785 rms_B_bonded: 6.67 restraints_weight: 4.0000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1338 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= 0.118 Angle : 0.638 14.716 23824 Z= 0.320 Chirality : 0.041 0.149 2680 Planarity : 0.004 0.072 3172 Dihedral : 4.894 55.337 2521 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.37 % Favored : 86.05 % Rotamer: Outliers : 2.20 % Allowed : 16.45 % Favored : 81.35 % 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 aren not related in a simple way. whole: -1.24 (0.19), residues: 2278 helix: 1.82 (0.21), residues: 697 sheet: -0.80 (0.32), residues: 306 loop : -2.53 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.021 0.001 TYR A 906 PHE 0.011 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 covalent geometry : bond 0.00261 (17513) covalent geometry : angle 0.63767 (23816) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.51314 ( 8) hydrogen bonds : bond 0.03182 ( 589) hydrogen bonds : angle 4.16535 ( 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: 36 poor density : 71 time to evaluate : 0.684 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 681 MET cc_start: 0.9632 (tmm) cc_final: 0.9311 (tmm) REVERT: C 1444 GLU cc_start: 0.4598 (tp30) cc_final: 0.4338 (tp30) REVERT: H 129 PHE cc_start: 0.8192 (t80) cc_final: 0.7587 (t80) REVERT: H 173 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.4863 (t80) REVERT: L 155 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8483 (t) outliers start: 36 outliers final: 21 residues processed: 105 average time/residue: 0.1515 time to fit residues: 24.2489 Evaluate side-chains 95 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 762 VAL Chi-restraints excluded: chain H residue 5 GLN 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 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 155 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: 0.0060 chunk 131 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 179 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 207 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.051495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035393 restraints weight = 445668.656| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 11.39 r_work: 0.2668 rms_B_bonded: 10.23 restraints_weight: 2.0000 r_work: 0.2793 rms_B_bonded: 6.48 restraints_weight: 4.0000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17517 Z= 0.110 Angle : 0.641 14.971 23824 Z= 0.319 Chirality : 0.042 0.277 2680 Planarity : 0.004 0.071 3172 Dihedral : 4.822 55.593 2521 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.62 % Favored : 86.85 % Rotamer: Outliers : 1.97 % Allowed : 16.90 % Favored : 81.13 % 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 aren not related in a simple way. whole: -1.21 (0.19), residues: 2278 helix: 1.86 (0.21), residues: 698 sheet: -0.91 (0.31), residues: 315 loop : -2.50 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 76 TYR 0.021 0.001 TYR A 906 PHE 0.010 0.001 PHE B 157 TRP 0.010 0.001 TRP H 38 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00237 (17513) covalent geometry : angle 0.64106 (23816) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.66713 ( 8) hydrogen bonds : bond 0.02955 ( 589) hydrogen bonds : angle 4.08758 ( 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 105 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LEU cc_start: 0.9232 (tt) cc_final: 0.8731 (pp) REVERT: A 599 MET cc_start: 0.9167 (tmm) cc_final: 0.8827 (tmm) REVERT: A 681 MET cc_start: 0.9607 (tmm) cc_final: 0.9302 (tmm) REVERT: B 246 ARG cc_start: 0.8832 (ttt90) cc_final: 0.8597 (ttt-90) REVERT: C 1444 GLU cc_start: 0.4817 (tp30) cc_final: 0.4545 (tp30) REVERT: C 1475 HIS cc_start: 0.4062 (p90) cc_final: 0.3829 (p-80) REVERT: H 173 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.4734 (t80) REVERT: L 110 MET cc_start: 0.9105 (mmm) cc_final: 0.8701 (mmm) outliers start: 32 outliers final: 23 residues processed: 103 average time/residue: 0.1512 time to fit residues: 23.8304 Evaluate side-chains 96 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 835 VAL Chi-restraints excluded: chain A residue 839 VAL 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 388 LEU 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 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** 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 = 0.3434 r_free = 0.3434 target = 0.050505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034267 restraints weight = 424008.675| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 10.40 r_work: 0.2647 rms_B_bonded: 9.78 restraints_weight: 2.0000 r_work: 0.2766 rms_B_bonded: 6.41 restraints_weight: 4.0000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 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 = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17517 Z= 0.139 Angle : 0.659 14.923 23824 Z= 0.329 Chirality : 0.042 0.196 2680 Planarity : 0.004 0.073 3172 Dihedral : 4.903 56.791 2521 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.51 % Favored : 85.96 % Rotamer: Outliers : 2.08 % Allowed : 16.90 % Favored : 81.01 % 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 aren not related in a simple way. whole: -1.19 (0.19), residues: 2278 helix: 1.99 (0.21), residues: 690 sheet: -0.95 (0.31), residues: 320 loop : -2.52 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1439 TYR 0.020 0.001 TYR A 906 PHE 0.031 0.001 PHE H 129 TRP 0.008 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00315 (17513) covalent geometry : angle 0.65948 (23816) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.62690 ( 8) hydrogen bonds : bond 0.03372 ( 589) hydrogen bonds : angle 4.11711 ( 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: 34 poor density : 72 time to evaluate : 0.651 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 233 MET cc_start: 0.9354 (tpp) cc_final: 0.9063 (ttm) REVERT: A 599 MET cc_start: 0.9194 (tmm) cc_final: 0.8865 (tmm) REVERT: A 681 MET cc_start: 0.9622 (tmm) cc_final: 0.9315 (tmm) REVERT: A 791 MET cc_start: 0.8259 (mmm) cc_final: 0.7262 (mmm) REVERT: C 1444 GLU cc_start: 0.4600 (tp30) cc_final: 0.4319 (tp30) REVERT: H 173 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.4954 (t80) outliers start: 34 outliers final: 28 residues processed: 103 average time/residue: 0.1584 time to fit residues: 24.6470 Evaluate side-chains 101 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 724 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 181 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 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 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: 0.7980 chunk 39 optimal weight: 0.0170 chunk 61 optimal weight: 0.4980 chunk 158 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 148 optimal weight: 0.2980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.051491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035137 restraints weight = 449776.134| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 10.93 r_work: 0.2684 rms_B_bonded: 10.17 restraints_weight: 2.0000 r_work: 0.2805 rms_B_bonded: 6.59 restraints_weight: 4.0000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 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 = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17517 Z= 0.108 Angle : 0.644 14.983 23824 Z= 0.321 Chirality : 0.042 0.185 2680 Planarity : 0.004 0.070 3172 Dihedral : 4.806 57.036 2521 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.48 % Favored : 86.94 % Rotamer: Outliers : 1.86 % Allowed : 17.18 % Favored : 80.96 % 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 aren not related in a simple way. whole: -1.18 (0.19), residues: 2278 helix: 1.99 (0.21), residues: 690 sheet: -1.00 (0.30), residues: 324 loop : -2.48 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C1439 TYR 0.019 0.001 TYR A 906 PHE 0.010 0.001 PHE B 157 TRP 0.008 0.001 TRP A 429 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00237 (17513) covalent geometry : angle 0.64361 (23816) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.67849 ( 8) hydrogen bonds : bond 0.02878 ( 589) hydrogen bonds : angle 4.01250 ( 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 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LEU cc_start: 0.9232 (tt) cc_final: 0.8766 (pp) REVERT: A 631 MET cc_start: 0.9498 (mtt) cc_final: 0.9244 (mtt) REVERT: A 681 MET cc_start: 0.9623 (tmm) cc_final: 0.9295 (tmm) REVERT: A 690 MET cc_start: 0.7061 (mmt) cc_final: 0.6817 (mmp) REVERT: A 791 MET cc_start: 0.8228 (mmm) cc_final: 0.7280 (mmm) REVERT: C 1444 GLU cc_start: 0.4542 (tp30) cc_final: 0.4262 (tp30) REVERT: H 129 PHE cc_start: 0.8179 (t80) cc_final: 0.7755 (t80) REVERT: H 173 PHE cc_start: 0.5938 (OUTLIER) cc_final: 0.4790 (t80) REVERT: L 110 MET cc_start: 0.9068 (mmm) cc_final: 0.8694 (mmm) REVERT: L 177 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8540 (pp30) outliers start: 30 outliers final: 25 residues processed: 100 average time/residue: 0.1501 time to fit residues: 22.5358 Evaluate side-chains 97 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 724 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL 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 388 LEU 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 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 5 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 0.0050 chunk 137 optimal weight: 0.2980 chunk 96 optimal weight: 0.0270 chunk 46 optimal weight: 0.0980 chunk 7 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 overall best weight: 0.0850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.052509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036495 restraints weight = 477072.236| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 12.10 r_work: 0.2711 rms_B_bonded: 10.54 restraints_weight: 2.0000 r_work: 0.2839 rms_B_bonded: 6.67 restraints_weight: 4.0000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17517 Z= 0.108 Angle : 0.640 14.307 23824 Z= 0.317 Chirality : 0.041 0.176 2680 Planarity : 0.004 0.067 3172 Dihedral : 4.676 56.747 2521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.39 % Favored : 87.12 % Rotamer: Outliers : 1.69 % Allowed : 17.30 % Favored : 81.01 % 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 aren not related in a simple way. whole: -1.12 (0.19), residues: 2278 helix: 2.02 (0.21), residues: 684 sheet: -0.74 (0.32), residues: 305 loop : -2.47 (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 0.010 0.001 PHE B 264 TRP 0.012 0.001 TRP A 429 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00232 (17513) covalent geometry : angle 0.64007 (23816) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.66670 ( 8) hydrogen bonds : bond 0.02640 ( 589) hydrogen bonds : angle 3.94748 ( 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 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.708 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 53 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 535 LEU cc_start: 0.9186 (tt) cc_final: 0.8736 (pp) REVERT: A 631 MET cc_start: 0.9471 (mtt) cc_final: 0.9249 (mtt) REVERT: A 681 MET cc_start: 0.9625 (tmm) cc_final: 0.9307 (tmm) REVERT: A 791 MET cc_start: 0.8141 (mmm) cc_final: 0.7213 (mmm) REVERT: A 901 PHE cc_start: 0.7655 (m-80) cc_final: 0.7352 (m-80) REVERT: C 1444 GLU cc_start: 0.4845 (tp30) cc_final: 0.4570 (tp30) REVERT: H 129 PHE cc_start: 0.8089 (t80) cc_final: 0.7722 (t80) REVERT: H 173 PHE cc_start: 0.5866 (OUTLIER) cc_final: 0.4612 (t80) REVERT: L 110 MET cc_start: 0.9025 (mmm) cc_final: 0.8702 (mmm) REVERT: L 177 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8550 (pp30) outliers start: 27 outliers final: 21 residues processed: 101 average time/residue: 0.1472 time to fit residues: 22.6952 Evaluate side-chains 97 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 353 LEU 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 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR 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 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 185 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.051556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035283 restraints weight = 438137.788| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 10.72 r_work: 0.2689 rms_B_bonded: 9.79 restraints_weight: 2.0000 r_work: 0.2812 rms_B_bonded: 6.31 restraints_weight: 4.0000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 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 = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1856 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= 0.120 Angle : 0.645 14.696 23824 Z= 0.321 Chirality : 0.042 0.180 2680 Planarity : 0.004 0.069 3172 Dihedral : 4.557 56.355 2521 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.66 % Favored : 86.98 % Rotamer: Outliers : 1.46 % Allowed : 17.58 % Favored : 80.96 % 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 aren not related in a simple way. whole: -1.10 (0.19), residues: 2278 helix: 2.11 (0.21), residues: 685 sheet: -0.93 (0.31), residues: 315 loop : -2.46 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 732 TYR 0.019 0.001 TYR A 906 PHE 0.008 0.001 PHE A 264 TRP 0.008 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00270 (17513) covalent geometry : angle 0.64538 (23816) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.61154 ( 8) hydrogen bonds : bond 0.02933 ( 589) hydrogen bonds : angle 3.92238 ( 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 92 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.677 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 535 LEU cc_start: 0.9221 (tt) cc_final: 0.8757 (pp) REVERT: A 631 MET cc_start: 0.9487 (mtt) cc_final: 0.9246 (mtt) REVERT: A 681 MET cc_start: 0.9634 (tmm) cc_final: 0.9315 (tmm) REVERT: A 791 MET cc_start: 0.8269 (mmm) cc_final: 0.7399 (mmm) REVERT: B 246 ARG cc_start: 0.8964 (ttt-90) cc_final: 0.8615 (ttt90) REVERT: C 1444 GLU cc_start: 0.4724 (tp30) cc_final: 0.4443 (tp30) REVERT: H 173 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.4755 (t80) outliers start: 23 outliers final: 22 residues processed: 91 average time/residue: 0.1274 time to fit residues: 17.8929 Evaluate side-chains 92 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 388 LEU 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 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR 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 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 84 optimal weight: 0.1980 chunk 120 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 145 optimal weight: 0.3980 chunk 98 optimal weight: 0.2980 chunk 24 optimal weight: 0.0000 chunk 207 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 600 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 = 0.3485 r_free = 0.3485 target = 0.052105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.036090 restraints weight = 462112.885| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 11.76 r_work: 0.2696 rms_B_bonded: 10.40 restraints_weight: 2.0000 r_work: 0.2823 rms_B_bonded: 6.61 restraints_weight: 4.0000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 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 = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17517 Z= 0.105 Angle : 0.636 14.616 23824 Z= 0.316 Chirality : 0.041 0.169 2680 Planarity : 0.004 0.068 3172 Dihedral : 4.470 56.050 2521 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.08 % Favored : 87.47 % Rotamer: Outliers : 1.80 % Allowed : 17.18 % Favored : 81.01 % 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 aren not related in a simple way. whole: -1.08 (0.19), residues: 2278 helix: 2.14 (0.21), residues: 676 sheet: -0.76 (0.32), residues: 305 loop : -2.45 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1439 TYR 0.019 0.001 TYR A 906 PHE 0.027 0.001 PHE H 129 TRP 0.010 0.001 TRP A 429 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00230 (17513) covalent geometry : angle 0.63561 (23816) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.63228 ( 8) hydrogen bonds : bond 0.02683 ( 589) hydrogen bonds : angle 3.87841 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7207.64 seconds wall clock time: 123 minutes 21.15 seconds (7401.15 seconds total)