Starting phenix.real_space_refine on Mon Nov 18 19:45:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_41496.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_41496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_41496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_41496.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpx_41496/11_2024/8tpx_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 18.60, per 1000 atoms: 1.08 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: 4.56 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: 1.82 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: 5.52 Time building geometry restraints manager: 5.23 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: 9.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 50.910 Find NCS groups from input model: 0.740 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.310 ------------------------------------------------------------------------------- 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 17513 Z= 0.220 Angle : 0.692 12.883 23816 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 *********************** 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 : 2.117 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: 0.3679 time to fit residues: 45.3130 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 : 2.049 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 17513 Z= 0.200 Angle : 0.655 13.917 23816 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 : 10.04 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 *********************** 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 : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.9236 (tmm) cc_final: 0.8893 (tmm) REVERT: A 791 MET cc_start: 0.8387 (mmm) cc_final: 0.7530 (mmm) REVERT: H 129 PHE cc_start: 0.8421 (t80) cc_final: 0.7388 (t80) REVERT: L 155 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8588 (t) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.3341 time to fit residues: 51.9370 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 : 1.983 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.0040 chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17513 Z= 0.194 Angle : 0.640 14.081 23816 Z= 0.325 Chirality : 0.042 0.204 2680 Planarity : 0.004 0.079 3172 Dihedral : 5.117 58.147 2523 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.55 % Favored : 85.78 % Rotamer: Outliers : 2.14 % Allowed : 15.72 % 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: -1.30 (0.18), residues: 2278 helix: 1.72 (0.21), residues: 701 sheet: -0.94 (0.31), residues: 303 loop : -2.51 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 PHE 0.015 0.001 PHE B 157 TYR 0.021 0.001 TYR A 906 ARG 0.007 0.000 ARG C1458 *********************** 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: 34 poor density : 71 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.9208 (tmm) cc_final: 0.8829 (tmm) REVERT: H 129 PHE cc_start: 0.8285 (t80) cc_final: 0.7307 (t80) REVERT: L 155 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8618 (t) outliers start: 34 outliers final: 20 residues processed: 102 average time/residue: 0.3353 time to fit residues: 52.7594 Evaluate side-chains 93 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 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 73 TRP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 585 PHE Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 106 optimal weight: 0.0010 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 206 optimal weight: 0.0020 chunk 218 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17513 Z= 0.172 Angle : 0.632 15.994 23816 Z= 0.319 Chirality : 0.042 0.150 2680 Planarity : 0.004 0.074 3172 Dihedral : 5.069 59.495 2523 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.97 % Favored : 86.49 % 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: -1.27 (0.18), residues: 2278 helix: 1.80 (0.21), residues: 694 sheet: -0.89 (0.32), residues: 295 loop : -2.51 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.006 0.001 HIS B 519 PHE 0.013 0.001 PHE B 157 TYR 0.031 0.001 TYR B 802 ARG 0.009 0.000 ARG C1439 *********************** 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 110 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.967 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 390 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9279 (tttm) REVERT: A 599 MET cc_start: 0.9125 (tmm) cc_final: 0.8915 (tmm) REVERT: A 681 MET cc_start: 0.9587 (tmm) cc_final: 0.9250 (tmm) REVERT: H 129 PHE cc_start: 0.8214 (t80) cc_final: 0.7611 (t80) REVERT: L 155 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8710 (t) outliers start: 35 outliers final: 23 residues processed: 107 average time/residue: 0.3191 time to fit residues: 52.4006 Evaluate side-chains 98 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 390 LYS 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 388 LEU 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 99 TYR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17513 Z= 0.263 Angle : 0.684 14.717 23816 Z= 0.344 Chirality : 0.042 0.194 2680 Planarity : 0.005 0.076 3172 Dihedral : 5.104 56.946 2521 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.77 % Favored : 85.70 % Rotamer: Outliers : 2.31 % Allowed : 16.34 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.19), residues: 2278 helix: 1.84 (0.21), residues: 694 sheet: -1.09 (0.30), residues: 335 loop : -2.55 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.006 0.001 HIS A 651 PHE 0.011 0.001 PHE B 157 TYR 0.020 0.002 TYR A 906 ARG 0.008 0.000 ARG C1439 *********************** 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 109 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.9151 (tpp) cc_final: 0.8868 (ttm) REVERT: A 390 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9316 (tttm) REVERT: A 599 MET cc_start: 0.9153 (tmm) cc_final: 0.8875 (tmm) REVERT: A 681 MET cc_start: 0.9608 (tmm) cc_final: 0.9269 (tmm) REVERT: C 1458 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8334 (mtt90) REVERT: H 129 PHE cc_start: 0.8179 (t80) cc_final: 0.7604 (t80) REVERT: H 173 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5364 (t80) outliers start: 38 outliers final: 27 residues processed: 106 average time/residue: 0.3172 time to fit residues: 53.0249 Evaluate side-chains 99 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 390 LYS 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 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 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 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 73 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17513 Z= 0.223 Angle : 0.674 16.427 23816 Z= 0.336 Chirality : 0.042 0.242 2680 Planarity : 0.004 0.074 3172 Dihedral : 5.092 57.881 2521 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.24 % Favored : 86.18 % Rotamer: Outliers : 2.14 % Allowed : 16.85 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.19), residues: 2278 helix: 1.84 (0.21), residues: 696 sheet: -0.95 (0.31), residues: 311 loop : -2.55 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.006 0.001 HIS B 519 PHE 0.012 0.001 PHE B 157 TYR 0.020 0.001 TYR A 906 ARG 0.011 0.000 ARG C1439 *********************** 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 106 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 1.966 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: 0.9070 (ttt) cc_final: 0.8737 (ttt) REVERT: A 233 MET cc_start: 0.9155 (tpp) cc_final: 0.8868 (ttm) REVERT: A 599 MET cc_start: 0.9192 (tmm) cc_final: 0.8896 (tmm) REVERT: A 681 MET cc_start: 0.9610 (tmm) cc_final: 0.9261 (tmm) REVERT: C 1458 ARG cc_start: 0.8872 (mmm-85) cc_final: 0.8476 (mmm-85) REVERT: C 1475 HIS cc_start: 0.4377 (p90) cc_final: 0.4109 (p-80) REVERT: H 173 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5362 (t80) REVERT: L 110 MET cc_start: 0.8804 (mmm) cc_final: 0.8536 (mmm) outliers start: 35 outliers final: 28 residues processed: 103 average time/residue: 0.3247 time to fit residues: 50.9732 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 : 1.908 ------------------------------------------------------------------------------- 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 98 ASP 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 H residue 5 GLN Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 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 210 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 122 optimal weight: 0.3980 chunk 217 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 overall best weight: 1.0500 ------------------------------------------------------------------------------- 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** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17513 Z= 0.233 Angle : 0.679 16.875 23816 Z= 0.338 Chirality : 0.043 0.178 2680 Planarity : 0.004 0.074 3172 Dihedral : 5.134 59.140 2521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.95 % Favored : 85.52 % Rotamer: Outliers : 2.20 % Allowed : 17.18 % 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: -1.29 (0.19), residues: 2278 helix: 1.87 (0.21), residues: 694 sheet: -1.06 (0.31), residues: 318 loop : -2.55 (0.17), residues: 1266 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 0.032 0.001 PHE H 129 TYR 0.021 0.001 TYR A 906 ARG 0.010 0.000 ARG B 732 *********************** 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: 36 poor density : 71 time to evaluate : 1.861 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: 0.9125 (ttt) cc_final: 0.8858 (ttt) REVERT: A 233 MET cc_start: 0.9153 (tpp) cc_final: 0.8867 (ttm) REVERT: A 681 MET cc_start: 0.9605 (tmm) cc_final: 0.9265 (tmm) REVERT: A 791 MET cc_start: 0.8278 (mmm) cc_final: 0.7656 (mmm) REVERT: C 1458 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8463 (mtt90) REVERT: C 1475 HIS cc_start: 0.4549 (p90) cc_final: 0.4287 (p-80) REVERT: H 173 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5488 (t80) outliers start: 36 outliers final: 31 residues processed: 104 average time/residue: 0.2966 time to fit residues: 48.4952 Evaluate side-chains 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 98 ASP 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 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17513 Z= 0.210 Angle : 0.670 17.339 23816 Z= 0.334 Chirality : 0.042 0.176 2680 Planarity : 0.004 0.073 3172 Dihedral : 5.110 59.952 2521 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.37 % Favored : 86.14 % Rotamer: Outliers : 2.25 % Allowed : 17.30 % Favored : 80.45 % 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: -1.25 (0.19), residues: 2278 helix: 1.98 (0.21), residues: 687 sheet: -1.08 (0.31), residues: 313 loop : -2.54 (0.17), residues: 1278 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 0.011 0.001 PHE B 157 TYR 0.020 0.001 TYR A 906 ARG 0.012 0.000 ARG C1439 *********************** 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 107 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.9112 (ttt) cc_final: 0.8865 (ttt) REVERT: A 233 MET cc_start: 0.9153 (tpp) cc_final: 0.8884 (ttm) REVERT: A 535 LEU cc_start: 0.9350 (tt) cc_final: 0.8856 (pp) REVERT: A 599 MET cc_start: 0.9067 (tmm) cc_final: 0.8733 (tmm) REVERT: A 631 MET cc_start: 0.9408 (mtt) cc_final: 0.9150 (mtt) REVERT: A 681 MET cc_start: 0.9610 (tmm) cc_final: 0.9266 (tmm) REVERT: C 1458 ARG cc_start: 0.8938 (mmm-85) cc_final: 0.8642 (mtt90) REVERT: C 1475 HIS cc_start: 0.4466 (p90) cc_final: 0.4202 (p-80) REVERT: H 173 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5398 (t80) REVERT: L 110 MET cc_start: 0.8775 (mmm) cc_final: 0.8535 (mmm) outliers start: 37 outliers final: 33 residues processed: 103 average time/residue: 0.3060 time to fit residues: 49.5249 Evaluate side-chains 102 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 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 98 ASP 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 519 HIS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 49 TRP 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 208 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 122 optimal weight: 0.0020 chunk 88 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 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** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17513 Z= 0.181 Angle : 0.667 17.701 23816 Z= 0.330 Chirality : 0.042 0.192 2680 Planarity : 0.004 0.071 3172 Dihedral : 5.029 59.806 2521 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.24 % Favored : 86.18 % Rotamer: Outliers : 2.08 % Allowed : 17.58 % Favored : 80.34 % 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: -1.23 (0.19), residues: 2278 helix: 1.99 (0.21), residues: 691 sheet: -1.08 (0.31), residues: 320 loop : -2.53 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 54 HIS 0.005 0.001 HIS B 519 PHE 0.031 0.001 PHE H 129 TYR 0.021 0.001 TYR A 906 ARG 0.014 0.000 ARG C1439 *********************** 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 105 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 2.131 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: 0.9090 (ttt) cc_final: 0.8848 (ttt) REVERT: A 233 MET cc_start: 0.9183 (tpp) cc_final: 0.8893 (ttm) REVERT: A 535 LEU cc_start: 0.9325 (tt) cc_final: 0.8805 (pp) REVERT: A 681 MET cc_start: 0.9610 (tmm) cc_final: 0.9256 (tmm) REVERT: A 791 MET cc_start: 0.8135 (mmm) cc_final: 0.7484 (mmm) REVERT: C 1458 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8630 (mtt90) REVERT: C 1475 HIS cc_start: 0.4478 (p90) cc_final: 0.4216 (p-80) REVERT: H 63 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8797 (tp30) REVERT: H 129 PHE cc_start: 0.8219 (t80) cc_final: 0.7837 (t80) REVERT: H 173 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5276 (t80) REVERT: L 177 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8385 (pp30) outliers start: 34 outliers final: 30 residues processed: 103 average time/residue: 0.3250 time to fit residues: 51.4640 Evaluate side-chains 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 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 38 TRP Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 173 PHE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 179 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 190 optimal weight: 0.4980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17513 Z= 0.175 Angle : 0.665 17.383 23816 Z= 0.328 Chirality : 0.042 0.177 2680 Planarity : 0.004 0.071 3172 Dihedral : 4.956 59.740 2521 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.06 % Favored : 86.36 % Rotamer: Outliers : 2.03 % Allowed : 17.75 % Favored : 80.23 % 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: 2.02 (0.21), residues: 690 sheet: -1.06 (0.31), residues: 320 loop : -2.53 (0.17), residues: 1268 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 0.029 0.001 PHE H 129 TYR 0.020 0.001 TYR A 906 ARG 0.013 0.000 ARG C1439 ********************** 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 103 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 1.956 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: 0.9069 (ttt) cc_final: 0.8824 (ttt) REVERT: A 535 LEU cc_start: 0.9313 (tt) cc_final: 0.8795 (pp) REVERT: A 631 MET cc_start: 0.9388 (mtt) cc_final: 0.9121 (mtt) REVERT: A 681 MET cc_start: 0.9611 (tmm) cc_final: 0.9243 (tmm) REVERT: A 791 MET cc_start: 0.8113 (mmm) cc_final: 0.7490 (mmm) REVERT: C 1475 HIS cc_start: 0.4632 (p90) cc_final: 0.4402 (p-80) REVERT: H 129 PHE cc_start: 0.8178 (t80) cc_final: 0.7811 (t80) REVERT: H 173 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5302 (t80) REVERT: L 110 MET cc_start: 0.8715 (mmm) cc_final: 0.8446 (mmm) REVERT: L 177 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8394 (pp30) outliers start: 33 outliers final: 30 residues processed: 101 average time/residue: 0.3242 time to fit residues: 50.4435 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 : 2.128 ------------------------------------------------------------------------------- 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 549 VAL Chi-restraints excluded: chain A residue 550 GLU 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 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 177 GLN Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 179 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 157 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034337 restraints weight = 434175.256| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 10.63 r_work: 0.2652 rms_B_bonded: 9.77 restraints_weight: 2.0000 r_work: 0.2773 rms_B_bonded: 6.40 restraints_weight: 4.0000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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 = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17513 Z= 0.179 Angle : 0.660 16.977 23816 Z= 0.326 Chirality : 0.042 0.197 2680 Planarity : 0.004 0.072 3172 Dihedral : 4.920 59.559 2521 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.53 % Allowed : 13.15 % Favored : 86.32 % Rotamer: Outliers : 2.08 % Allowed : 17.63 % 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: -1.19 (0.19), residues: 2278 helix: 2.04 (0.21), residues: 691 sheet: -1.07 (0.31), residues: 325 loop : -2.51 (0.17), residues: 1262 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 0.027 0.001 PHE H 129 TYR 0.020 0.001 TYR A 906 ARG 0.013 0.000 ARG C1439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4181.27 seconds wall clock time: 77 minutes 23.95 seconds (4643.95 seconds total)