Starting phenix.real_space_refine on Sun May 18 17:57:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpx_41496/05_2025/8tpx_41496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpx_41496/05_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_41496/05_2025/8tpx_41496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpx_41496/05_2025/8tpx_41496.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpx_41496/05_2025/8tpx_41496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpx_41496/05_2025/8tpx_41496.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.48, per 1000 atoms: 1.13 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: 4.76 Conformation dependent library (CDL) restraints added in 4.3 seconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 34.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 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: 6.24 Time building geometry restraints manager: 5.58 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: 8.460 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: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.330 Process input model: 55.230 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (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 TRP 0.015 0.001 TRP A 54 HIS 0.007 0.001 HIS A 832 PHE 0.011 0.001 PHE B 157 TYR 0.019 0.001 TYR A 906 ARG 0.007 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.16714 ( 589) hydrogen bonds : angle 6.45322 ( 1650) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.69614 ( 8) covalent geometry : bond 0.00321 (17513) covalent geometry : angle 0.69165 (23816) *********************** 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 : 1.987 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: 0.3580 time to fit residues: 44.0927 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 : 1.929 ------------------------------------------------------------------------------- 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 190 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 205 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 = 0.3452 r_free = 0.3452 target = 0.050988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034642 restraints weight = 510795.213| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 11.63 r_work: 0.2641 rms_B_bonded: 10.37 restraints_weight: 2.0000 r_work: 0.2768 rms_B_bonded: 6.56 restraints_weight: 4.0000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17517 Z= 0.134 Angle : 0.655 13.917 23824 Z= 0.334 Chirality : 0.042 0.279 2680 Planarity : 0.005 0.079 3172 Dihedral : 5.190 58.023 2527 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.37 % Favored : 86.05 % Rotamer: Outliers : 1.86 % Allowed : 16.06 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2278 helix: 1.66 (0.21), residues: 700 sheet: -0.97 (0.31), residues: 307 loop : -2.50 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 PHE 0.020 0.001 PHE B 157 TYR 0.020 0.001 TYR A 906 ARG 0.006 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 589) hydrogen bonds : angle 4.60034 ( 1650) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.58709 ( 8) covalent geometry : bond 0.00293 (17513) covalent geometry : angle 0.65528 (23816) *********************** 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 104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.9360 (tmm) cc_final: 0.9006 (tmm) REVERT: A 791 MET cc_start: 0.8384 (mmm) cc_final: 0.7517 (mmm) REVERT: C 1444 GLU cc_start: 0.4641 (tp30) cc_final: 0.4343 (tp30) REVERT: H 129 PHE cc_start: 0.8448 (t80) cc_final: 0.7375 (t80) REVERT: L 155 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8322 (t) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.3005 time to fit residues: 46.6007 Evaluate side-chains 85 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 473 VAL 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 129 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** B 121 GLN ** 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 = 0.3418 r_free = 0.3418 target = 0.049960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.033852 restraints weight = 439201.227| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 10.80 r_work: 0.2614 rms_B_bonded: 9.79 restraints_weight: 2.0000 r_work: 0.2737 rms_B_bonded: 6.26 restraints_weight: 4.0000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17517 Z= 0.162 Angle : 0.668 14.538 23824 Z= 0.340 Chirality : 0.042 0.200 2680 Planarity : 0.005 0.081 3172 Dihedral : 5.243 59.185 2523 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.95 % Favored : 85.43 % Rotamer: Outliers : 2.20 % Allowed : 15.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2278 helix: 1.72 (0.21), residues: 699 sheet: -1.09 (0.31), residues: 310 loop : -2.52 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 PHE 0.015 0.001 PHE B 157 TYR 0.020 0.001 TYR A 906 ARG 0.007 0.000 ARG C1458 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 589) hydrogen bonds : angle 4.45163 ( 1650) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.56072 ( 8) covalent geometry : bond 0.00362 (17513) covalent geometry : angle 0.66757 (23816) *********************** 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 105 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 1.862 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 233 MET cc_start: 0.9341 (tpp) cc_final: 0.9046 (ttm) REVERT: A 599 MET cc_start: 0.9400 (tmm) cc_final: 0.9015 (tmm) REVERT: C 1439 ARG cc_start: 0.8971 (mtm110) cc_final: 0.8747 (mtm110) REVERT: H 129 PHE cc_start: 0.8309 (t80) cc_final: 0.7678 (t80) outliers start: 36 outliers final: 22 residues processed: 102 average time/residue: 0.3030 time to fit residues: 47.6679 Evaluate side-chains 91 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE 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 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 159 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 0.0070 chunk 65 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.050813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034667 restraints weight = 480550.997| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 11.66 r_work: 0.2633 rms_B_bonded: 10.46 restraints_weight: 2.0000 r_work: 0.2761 rms_B_bonded: 6.55 restraints_weight: 4.0000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 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 = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1275 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= 0.118 Angle : 0.637 15.289 23824 Z= 0.323 Chirality : 0.042 0.150 2680 Planarity : 0.004 0.076 3172 Dihedral : 5.175 57.349 2523 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.93 % Favored : 86.45 % Rotamer: Outliers : 2.14 % Allowed : 15.89 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 2278 helix: 1.77 (0.21), residues: 694 sheet: -1.00 (0.31), residues: 315 loop : -2.52 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.006 0.001 HIS B 519 PHE 0.014 0.001 PHE B 157 TYR 0.031 0.001 TYR B 802 ARG 0.005 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 589) hydrogen bonds : angle 4.26584 ( 1650) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.51965 ( 8) covalent geometry : bond 0.00260 (17513) covalent geometry : angle 0.63696 (23816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8936 (ttt) cc_final: 0.8623 (ttt) REVERT: A 681 MET cc_start: 0.9607 (tmm) cc_final: 0.9301 (tmm) REVERT: C 1439 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8680 (mtm110) REVERT: C 1444 GLU cc_start: 0.4872 (tp30) cc_final: 0.4600 (tp30) REVERT: C 1458 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8120 (mmm-85) REVERT: H 129 PHE cc_start: 0.8285 (t80) cc_final: 0.7716 (t80) REVERT: H 173 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.4917 (t80) REVERT: L 110 MET cc_start: 0.9160 (mmm) cc_final: 0.8748 (mmm) outliers start: 35 outliers final: 26 residues processed: 104 average time/residue: 0.3054 time to fit residues: 49.1032 Evaluate side-chains 99 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 73 TRP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 68 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 211 optimal weight: 0.4980 chunk 198 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3397 r_free = 0.3397 target = 0.049462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033207 restraints weight = 466666.366| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 11.26 r_work: 0.2578 rms_B_bonded: 10.05 restraints_weight: 2.0000 r_work: 0.2700 rms_B_bonded: 6.45 restraints_weight: 4.0000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17517 Z= 0.192 Angle : 0.699 15.129 23824 Z= 0.352 Chirality : 0.043 0.176 2680 Planarity : 0.005 0.079 3172 Dihedral : 5.234 57.820 2521 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 14.17 % Favored : 85.30 % Rotamer: Outliers : 2.59 % Allowed : 16.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 2278 helix: 1.74 (0.21), residues: 700 sheet: -1.03 (0.31), residues: 314 loop : -2.57 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.005 0.001 HIS B 519 PHE 0.012 0.001 PHE B 157 TYR 0.021 0.002 TYR A 906 ARG 0.005 0.000 ARG C1458 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 589) hydrogen bonds : angle 4.37818 ( 1650) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.57723 ( 8) covalent geometry : bond 0.00429 (17513) covalent geometry : angle 0.69887 (23816) *********************** 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 114 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9066 (ttt) cc_final: 0.8790 (ttt) REVERT: A 233 MET cc_start: 0.9300 (tpp) cc_final: 0.9039 (ttm) REVERT: A 599 MET cc_start: 0.9242 (tmm) cc_final: 0.8873 (tmm) REVERT: A 791 MET cc_start: 0.8286 (mmm) cc_final: 0.7338 (mmm) REVERT: C 1444 GLU cc_start: 0.4807 (tp30) cc_final: 0.4501 (tp30) REVERT: H 129 PHE cc_start: 0.8247 (t80) cc_final: 0.7701 (t80) REVERT: H 173 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5323 (t80) outliers start: 43 outliers final: 31 residues processed: 110 average time/residue: 0.3171 time to fit residues: 53.8549 Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 220 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** 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 = 0.3436 r_free = 0.3436 target = 0.050566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034191 restraints weight = 433174.564| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 10.63 r_work: 0.2639 rms_B_bonded: 9.90 restraints_weight: 2.0000 r_work: 0.2760 rms_B_bonded: 6.43 restraints_weight: 4.0000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 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 = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17517 Z= 0.118 Angle : 0.665 17.019 23824 Z= 0.330 Chirality : 0.042 0.188 2680 Planarity : 0.004 0.075 3172 Dihedral : 5.092 57.903 2521 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.53 % Favored : 86.89 % Rotamer: Outliers : 2.20 % Allowed : 17.07 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2278 helix: 1.73 (0.21), residues: 696 sheet: -1.06 (0.32), residues: 302 loop : -2.54 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.007 0.001 HIS B 519 PHE 0.011 0.001 PHE B 157 TYR 0.021 0.001 TYR A 906 ARG 0.007 0.000 ARG B 732 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 589) hydrogen bonds : angle 4.20550 ( 1650) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.50632 ( 8) covalent geometry : bond 0.00260 (17513) covalent geometry : angle 0.66500 (23816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8934 (ttt) cc_final: 0.8656 (ttt) REVERT: A 535 LEU cc_start: 0.9350 (tt) cc_final: 0.8795 (pp) REVERT: A 599 MET cc_start: 0.9221 (tmm) cc_final: 0.8848 (tmm) REVERT: C 1444 GLU cc_start: 0.4724 (tp30) cc_final: 0.4426 (tp30) REVERT: C 1475 HIS cc_start: 0.3917 (p90) cc_final: 0.3681 (p-80) REVERT: H 21 ARG cc_start: 0.9055 (tpt170) cc_final: 0.8641 (tpt170) REVERT: H 173 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.5009 (t80) REVERT: L 110 MET cc_start: 0.9175 (mmm) cc_final: 0.8780 (mmm) outliers start: 36 outliers final: 30 residues processed: 103 average time/residue: 0.3071 time to fit residues: 48.3665 Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 536 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 73 TRP 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 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 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 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 220 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 130 optimal weight: 0.1980 chunk 131 optimal weight: 0.0470 chunk 212 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 117 optimal weight: 0.0070 chunk 125 optimal weight: 1.9990 overall best weight: 0.1234 ------------------------------------------------------------------------------- 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** ** 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 = 0.3474 r_free = 0.3474 target = 0.051805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035429 restraints weight = 444558.925| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 10.93 r_work: 0.2695 rms_B_bonded: 10.08 restraints_weight: 2.0000 r_work: 0.2820 rms_B_bonded: 6.50 restraints_weight: 4.0000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 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 = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17517 Z= 0.112 Angle : 0.653 16.386 23824 Z= 0.322 Chirality : 0.042 0.183 2680 Planarity : 0.004 0.070 3172 Dihedral : 4.858 57.964 2521 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.79 % Favored : 86.67 % Rotamer: Outliers : 2.08 % Allowed : 17.30 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 2278 helix: 1.95 (0.21), residues: 683 sheet: -0.93 (0.31), residues: 315 loop : -2.50 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 429 HIS 0.005 0.001 HIS B 519 PHE 0.030 0.001 PHE H 129 TYR 0.021 0.001 TYR A 906 ARG 0.012 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 589) hydrogen bonds : angle 4.07709 ( 1650) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.71072 ( 8) covalent geometry : bond 0.00237 (17513) covalent geometry : angle 0.65332 (23816) *********************** 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 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8864 (ttt) cc_final: 0.8596 (ttt) REVERT: A 535 LEU cc_start: 0.9272 (tt) cc_final: 0.8780 (pp) REVERT: A 795 GLU cc_start: 0.9581 (OUTLIER) cc_final: 0.9377 (tt0) REVERT: B 353 LEU cc_start: 0.8877 (mm) cc_final: 0.8605 (mm) REVERT: C 1444 GLU cc_start: 0.4755 (tp30) cc_final: 0.4472 (tp30) REVERT: C 1475 HIS cc_start: 0.3862 (p90) cc_final: 0.3622 (p-80) REVERT: H 129 PHE cc_start: 0.8052 (t80) cc_final: 0.7745 (t80) REVERT: H 173 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.4748 (t80) REVERT: L 177 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8538 (pp30) outliers start: 34 outliers final: 26 residues processed: 105 average time/residue: 0.3109 time to fit residues: 50.0007 Evaluate side-chains 100 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 795 GLU Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 1458 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 156 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.050541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.034199 restraints weight = 428357.137| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 10.43 r_work: 0.2646 rms_B_bonded: 9.72 restraints_weight: 2.0000 r_work: 0.2768 rms_B_bonded: 6.34 restraints_weight: 4.0000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17517 Z= 0.137 Angle : 0.659 16.809 23824 Z= 0.326 Chirality : 0.042 0.180 2680 Planarity : 0.004 0.073 3172 Dihedral : 4.913 58.176 2521 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.37 % Favored : 86.18 % Rotamer: Outliers : 2.25 % Allowed : 17.24 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 2278 helix: 1.99 (0.21), residues: 689 sheet: -1.03 (0.30), residues: 327 loop : -2.52 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.005 0.001 HIS B 519 PHE 0.024 0.001 PHE H 129 TYR 0.021 0.001 TYR A 906 ARG 0.008 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 589) hydrogen bonds : angle 4.08879 ( 1650) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.58625 ( 8) covalent geometry : bond 0.00309 (17513) covalent geometry : angle 0.65951 (23816) *********************** 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 108 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8914 (ttt) cc_final: 0.8631 (ttt) REVERT: A 233 MET cc_start: 0.9342 (tpp) cc_final: 0.9057 (ttm) REVERT: A 599 MET cc_start: 0.9242 (tmm) cc_final: 0.8913 (tmm) REVERT: C 1439 ARG cc_start: 0.8901 (mtm110) cc_final: 0.8690 (mtm110) REVERT: C 1444 GLU cc_start: 0.4673 (tp30) cc_final: 0.4396 (tp30) REVERT: H 173 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.4946 (t80) REVERT: L 110 MET cc_start: 0.9036 (mmm) cc_final: 0.8721 (mmm) outliers start: 37 outliers final: 33 residues processed: 105 average time/residue: 0.3204 time to fit residues: 51.3681 Evaluate side-chains 104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 216 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 169 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 116 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.3534 ------------------------------------------------------------------------------- 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** C1483 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.051384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.034889 restraints weight = 524901.136| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 11.70 r_work: 0.2663 rms_B_bonded: 10.47 restraints_weight: 2.0000 r_work: 0.2788 rms_B_bonded: 6.76 restraints_weight: 4.0000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 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 = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17517 Z= 0.107 Angle : 0.647 16.328 23824 Z= 0.319 Chirality : 0.041 0.175 2680 Planarity : 0.004 0.071 3172 Dihedral : 4.845 58.216 2521 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.48 % Favored : 86.98 % Rotamer: Outliers : 2.08 % Allowed : 17.35 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 2278 helix: 1.97 (0.21), residues: 689 sheet: -1.06 (0.31), residues: 318 loop : -2.50 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.006 0.001 HIS B 519 PHE 0.008 0.001 PHE B 157 TYR 0.021 0.001 TYR A 906 ARG 0.007 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 589) hydrogen bonds : angle 3.99792 ( 1650) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.67426 ( 8) covalent geometry : bond 0.00236 (17513) covalent geometry : angle 0.64748 (23816) *********************** 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: 34 poor density : 69 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8889 (ttt) cc_final: 0.8602 (ttt) REVERT: A 535 LEU cc_start: 0.9282 (tt) cc_final: 0.8809 (pp) REVERT: A 791 MET cc_start: 0.8168 (mmm) cc_final: 0.7489 (mmm) REVERT: B 246 ARG cc_start: 0.8855 (ttt90) cc_final: 0.8642 (ttt-90) REVERT: C 1439 ARG cc_start: 0.8860 (mtm110) cc_final: 0.8646 (mtm110) REVERT: C 1444 GLU cc_start: 0.4620 (tp30) cc_final: 0.4330 (tp30) REVERT: H 129 PHE cc_start: 0.8232 (t80) cc_final: 0.7793 (t80) REVERT: H 173 PHE cc_start: 0.5991 (OUTLIER) cc_final: 0.4821 (t80) REVERT: L 110 MET cc_start: 0.8998 (mmm) cc_final: 0.8656 (mmm) outliers start: 34 outliers final: 32 residues processed: 101 average time/residue: 0.3081 time to fit residues: 48.0983 Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 141 HIS Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 214 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 198 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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** ** B 121 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 = 0.3449 r_free = 0.3449 target = 0.051058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034507 restraints weight = 567299.963| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 11.97 r_work: 0.2647 rms_B_bonded: 10.78 restraints_weight: 2.0000 r_work: 0.2770 rms_B_bonded: 7.00 restraints_weight: 4.0000 r_work (final): 0.2770 ------------------------------------------------------------------------------- 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: 19 | |-----------------------------------------------------------------------------| |-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: 19 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17517 Z= 0.115 Angle : 0.655 16.409 23824 Z= 0.322 Chirality : 0.042 0.178 2680 Planarity : 0.004 0.072 3172 Dihedral : 4.818 58.363 2521 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.88 % Favored : 86.67 % Rotamer: Outliers : 2.08 % Allowed : 17.35 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2278 helix: 2.02 (0.21), residues: 689 sheet: -0.94 (0.31), residues: 314 loop : -2.50 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 PHE 0.008 0.001 PHE A 264 TYR 0.021 0.001 TYR A 906 ARG 0.006 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 589) hydrogen bonds : angle 3.98284 ( 1650) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.61792 ( 8) covalent geometry : bond 0.00259 (17513) covalent geometry : angle 0.65466 (23816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8914 (ttt) cc_final: 0.8641 (ttt) REVERT: A 535 LEU cc_start: 0.9293 (tt) cc_final: 0.8792 (pp) REVERT: A 690 MET cc_start: 0.7104 (mmp) cc_final: 0.6707 (mmp) REVERT: A 791 MET cc_start: 0.8195 (mmm) cc_final: 0.7531 (mmm) REVERT: C 1439 ARG cc_start: 0.8826 (mtm110) cc_final: 0.8606 (mtm110) REVERT: C 1444 GLU cc_start: 0.4528 (tp30) cc_final: 0.4243 (tp30) REVERT: H 129 PHE cc_start: 0.8217 (t80) cc_final: 0.7838 (t80) REVERT: H 173 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.4911 (t80) REVERT: L 110 MET cc_start: 0.9036 (mmm) cc_final: 0.8704 (mmm) outliers start: 34 outliers final: 32 residues processed: 101 average time/residue: 0.3009 time to fit residues: 46.7700 Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 141 HIS 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 724 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 1458 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 97 optimal weight: 0.0870 chunk 180 optimal weight: 0.7980 chunk 198 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 0.0030 chunk 115 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.4968 ------------------------------------------------------------------------------- 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** ** B 121 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 = 0.3454 r_free = 0.3454 target = 0.051205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034807 restraints weight = 479074.754| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 11.24 r_work: 0.2665 rms_B_bonded: 10.16 restraints_weight: 2.0000 r_work: 0.2789 rms_B_bonded: 6.55 restraints_weight: 4.0000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 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 = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17517 Z= 0.111 Angle : 0.652 16.247 23824 Z= 0.321 Chirality : 0.041 0.176 2680 Planarity : 0.004 0.072 3172 Dihedral : 4.705 58.150 2521 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.53 % Favored : 87.03 % Rotamer: Outliers : 2.03 % Allowed : 17.69 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 2278 helix: 2.00 (0.21), residues: 692 sheet: -0.92 (0.31), residues: 314 loop : -2.49 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.005 0.001 HIS B 519 PHE 0.015 0.001 PHE C1442 TYR 0.021 0.001 TYR A 906 ARG 0.007 0.000 ARG C1439 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 589) hydrogen bonds : angle 3.97070 ( 1650) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.60564 ( 8) covalent geometry : bond 0.00248 (17513) covalent geometry : angle 0.65231 (23816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13627.14 seconds wall clock time: 234 minutes 52.10 seconds (14092.10 seconds total)