Starting phenix.real_space_refine on Mon Feb 19 07:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ry3_24732/02_2024/7ry3_24732_trim_updated.pdb" } resolution = 2.91 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 ------------------------------------------------------------------------------- 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= 0.217 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 S 102 5.16 5 C 15423 2.51 5 N 3973 2.21 5 O 4463 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23964 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 7979 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 47, 'TRANS': 999} Chain: "B" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 7958 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 47, 'TRANS': 997} Chain: "C" Number of atoms: 8027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8027 Unusual residues: {'80P': 1} Classifications: {'peptide': 1048, 'undetermined': 1} Link IDs: {'PTRANS': 48, 'TRANS': 999, None: 1} Not linked: pdbres="PRO C1048 " pdbres="80P C1101 " Time building chain proxies: 11.81, per 1000 atoms: 0.49 Number of scatterers: 23964 At special positions: 0 Unit cell: (126.36, 124.2, 154.44, 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 102 16.00 F 3 9.00 O 4463 8.00 N 3973 7.00 C 15423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.15 Conformation dependent library (CDL) restraints added in 4.7 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 25 sheets defined 55.3% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.581A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.616A pdb=" N GLN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.535A pdb=" N VAL A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.680A pdb=" N TYR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 4.019A pdb=" N LYS A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 removed outlier: 3.565A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 4.009A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.610A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.723A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.901A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 451 removed outlier: 3.567A pdb=" N GLN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 461 through 496 removed outlier: 3.661A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.853A pdb=" N ASP A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.602A pdb=" N VAL A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.807A pdb=" N ALA A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N MET A 657 " --> pdb=" O MET A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 676 No H-bonds generated for 'chain 'A' and resid 674 through 676' Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 778 through 781 Processing helix chain 'A' and resid 784 through 789 Processing helix chain 'A' and resid 802 through 805 No H-bonds generated for 'chain 'A' and resid 802 through 805' Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.638A pdb=" N LEU A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 867 through 897 removed outlier: 3.661A pdb=" N ALA A 878 " --> pdb=" O SER A 874 " (cutoff:3.500A) Proline residue: A 879 - end of helix Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 928 removed outlier: 4.076A pdb=" N GLY A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 966 removed outlier: 3.506A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1001 removed outlier: 4.706A pdb=" N ARG A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Proline residue: A 985 - end of helix Proline residue: A 999 - end of helix Processing helix chain 'A' and resid 1008 through 1027 removed outlier: 3.780A pdb=" N GLY A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1043 Proline residue: A1034 - end of helix removed outlier: 3.534A pdb=" N TYR A1037 " --> pdb=" O ILE A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.887A pdb=" N GLN B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 removed outlier: 4.819A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 190 through 196 removed outlier: 4.042A pdb=" N TYR B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 316 removed outlier: 4.282A pdb=" N LYS B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 386 removed outlier: 3.603A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.215A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 3.609A pdb=" N GLN B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 462 through 486 removed outlier: 3.512A pdb=" N THR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 510 through 539 removed outlier: 3.888A pdb=" N SER B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 645 through 658 removed outlier: 3.775A pdb=" N LEU B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET B 657 " --> pdb=" O MET B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 744 through 755 Processing helix chain 'B' and resid 778 through 781 No H-bonds generated for 'chain 'B' and resid 778 through 781' Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 802 through 805 No H-bonds generated for 'chain 'B' and resid 802 through 805' Processing helix chain 'B' and resid 838 through 855 removed outlier: 3.708A pdb=" N LEU B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix Processing helix chain 'B' and resid 866 through 897 removed outlier: 3.527A pdb=" N GLU B 870 " --> pdb=" O GLY B 866 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA B 878 " --> pdb=" O SER B 874 " (cutoff:3.500A) Proline residue: B 879 - end of helix removed outlier: 3.666A pdb=" N TYR B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 886 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 927 removed outlier: 3.973A pdb=" N VAL B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Proline residue: B 911 - end of helix removed outlier: 3.565A pdb=" N VAL B 914 " --> pdb=" O VAL B 910 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 917 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 967 Processing helix chain 'B' and resid 971 through 1001 removed outlier: 4.702A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Proline residue: B 985 - end of helix removed outlier: 3.650A pdb=" N THR B 990 " --> pdb=" O ILE B 986 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) Proline residue: B 999 - end of helix Processing helix chain 'B' and resid 1008 through 1043 removed outlier: 4.267A pdb=" N PHE B1031 " --> pdb=" O PHE B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.576A pdb=" N THR C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.780A pdb=" N GLN C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 113 removed outlier: 4.358A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.645A pdb=" N GLN C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 299 through 316 removed outlier: 4.306A pdb=" N LYS C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.723A pdb=" N PHE C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 386 removed outlier: 4.132A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 422 removed outlier: 4.311A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 458 removed outlier: 3.580A pdb=" N GLN C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.816A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 486 removed outlier: 3.646A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 510 through 538 Processing helix chain 'C' and resid 540 through 559 removed outlier: 3.555A pdb=" N GLN C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 603 Processing helix chain 'C' and resid 645 through 658 removed outlier: 4.098A pdb=" N ALA C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN C 656 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET C 657 " --> pdb=" O MET C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 710 removed outlier: 3.697A pdb=" N SER C 709 " --> pdb=" O LEU C 705 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 710 " --> pdb=" O GLY C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 744 through 754 Processing helix chain 'C' and resid 778 through 781 Processing helix chain 'C' and resid 784 through 789 Processing helix chain 'C' and resid 802 through 805 No H-bonds generated for 'chain 'C' and resid 802 through 805' Processing helix chain 'C' and resid 838 through 855 removed outlier: 4.214A pdb=" N LEU C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Proline residue: C 853 - end of helix Processing helix chain 'C' and resid 866 through 874 removed outlier: 3.616A pdb=" N SER C 874 " --> pdb=" O GLU C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 897 Processing helix chain 'C' and resid 902 through 927 removed outlier: 3.600A pdb=" N LEU C 908 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 909 " --> pdb=" O VAL C 906 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 910 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Proline residue: C 911 - end of helix removed outlier: 4.110A pdb=" N ILE C 915 " --> pdb=" O LEU C 912 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 916 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 920 " --> pdb=" O ALA C 917 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 923 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 924 " --> pdb=" O THR C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 966 Processing helix chain 'C' and resid 971 through 1001 removed outlier: 4.506A pdb=" N ARG C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Proline residue: C 985 - end of helix removed outlier: 3.594A pdb=" N ALA C 992 " --> pdb=" O MET C 988 " (cutoff:3.500A) Proline residue: C 999 - end of helix Processing helix chain 'C' and resid 1008 through 1043 removed outlier: 3.944A pdb=" N PHE C1031 " --> pdb=" O PHE C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.762A pdb=" N GLN A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 12.706A pdb=" N ARG A 816 " --> pdb=" O ASN A 827 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ASN A 827 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 818 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.517A pdb=" N GLN A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 141 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU A 325 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR A 143 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 323 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.900A pdb=" N ASN A 761 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 774 " --> pdb=" O TYR A 759 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR A 759 " --> pdb=" O VAL A 774 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.648A pdb=" N LYS A 631 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 610 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 629 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 612 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 627 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 718 through 720 removed outlier: 4.366A pdb=" N ASN A 827 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 725 through 732 Processing sheet with id= G, first strand: chain 'A' and resid 791 through 793 Processing sheet with id= H, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.596A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.736A pdb=" N GLN B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 321 through 325 removed outlier: 3.559A pdb=" N GLU B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.619A pdb=" N TYR B 182 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 771 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 761 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 774 " --> pdb=" O TYR B 759 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR B 759 " --> pdb=" O VAL B 774 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.768A pdb=" N LYS B 631 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 610 " --> pdb=" O PHE B 629 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE B 629 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 612 " --> pdb=" O ILE B 627 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 627 " --> pdb=" O THR B 612 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER B 614 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA B 625 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 824 through 830 removed outlier: 4.031A pdb=" N SER B 824 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 725 through 732 Processing sheet with id= O, first strand: chain 'B' and resid 791 through 793 Processing sheet with id= P, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.603A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.789A pdb=" N GLN C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 77 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.966A pdb=" N VAL C 769 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N MET C 184 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS C 771 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 186 " --> pdb=" O LYS C 771 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 773 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C 188 " --> pdb=" O TYR C 773 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN C 775 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.547A pdb=" N LYS C 631 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE C 610 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 629 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR C 612 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 627 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C 614 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA C 625 " --> pdb=" O SER C 614 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 825 through 830 Processing sheet with id= U, first strand: chain 'C' and resid 725 through 732 Processing sheet with id= V, first strand: chain 'C' and resid 791 through 793 Processing sheet with id= W, first strand: chain 'C' and resid 322 through 328 removed outlier: 6.338A pdb=" N VAL C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP C 328 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU C 137 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 289 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 141 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 287 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 215 through 218 removed outlier: 4.334A pdb=" N VAL C 216 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 234 " --> pdb=" O VAL C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.094A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1354 hydrogen bonds defined for protein. 3903 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: 9.70 Time building geometry restraints manager: 10.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4015 1.31 - 1.44: 6301 1.44 - 1.56: 13909 1.56 - 1.69: 19 1.69 - 1.81: 198 Bond restraints: 24442 Sorted by residual: bond pdb=" C04 80P C1101 " pdb=" C21 80P C1101 " ideal model delta sigma weight residual 1.360 1.675 -0.315 2.00e-02 2.50e+03 2.48e+02 bond pdb=" C08 80P C1101 " pdb=" C09 80P C1101 " ideal model delta sigma weight residual 1.332 1.647 -0.315 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C11 80P C1101 " pdb=" C12 80P C1101 " ideal model delta sigma weight residual 1.240 1.554 -0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C09 80P C1101 " pdb=" C10 80P C1101 " ideal model delta sigma weight residual 1.097 1.374 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C26 80P C1101 " pdb=" C30 80P C1101 " ideal model delta sigma weight residual 1.293 1.553 -0.260 2.00e-02 2.50e+03 1.70e+02 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 97.01 - 105.07: 629 105.07 - 113.12: 12617 113.12 - 121.17: 14406 121.17 - 129.23: 5441 129.23 - 137.28: 154 Bond angle restraints: 33247 Sorted by residual: angle pdb=" N VAL B 376 " pdb=" CA VAL B 376 " pdb=" C VAL B 376 " ideal model delta sigma weight residual 110.42 122.13 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N LYS C 796 " pdb=" CA LYS C 796 " pdb=" C LYS C 796 " ideal model delta sigma weight residual 113.30 97.52 15.78 1.34e+00 5.57e-01 1.39e+02 angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 110.72 120.59 -9.87 1.01e+00 9.80e-01 9.54e+01 angle pdb=" N GLN A 276 " pdb=" CA GLN A 276 " pdb=" C GLN A 276 " ideal model delta sigma weight residual 111.36 121.72 -10.36 1.09e+00 8.42e-01 9.03e+01 angle pdb=" N ALA A 236 " pdb=" CA ALA A 236 " pdb=" C ALA A 236 " ideal model delta sigma weight residual 108.00 121.88 -13.88 1.48e+00 4.57e-01 8.79e+01 ... (remaining 33242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 14058 26.60 - 53.19: 463 53.19 - 79.78: 40 79.78 - 106.38: 1 106.38 - 132.97: 1 Dihedral angle restraints: 14563 sinusoidal: 5582 harmonic: 8981 Sorted by residual: dihedral pdb=" C VAL A 172 " pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" CB VAL A 172 " ideal model delta harmonic sigma weight residual -122.00 -136.68 14.68 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C VAL C 454 " pdb=" N VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual -122.00 -135.39 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N VAL C 454 " pdb=" C VAL C 454 " pdb=" CA VAL C 454 " pdb=" CB VAL C 454 " ideal model delta harmonic sigma weight residual 123.40 136.50 -13.10 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 14560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.123: 3912 1.123 - 2.246: 0 2.246 - 3.368: 0 3.368 - 4.491: 0 4.491 - 5.614: 1 Chirality restraints: 3913 Sorted by residual: chirality pdb=" C08 80P C1101 " pdb=" C07 80P C1101 " pdb=" C09 80P C1101 " pdb=" C21 80P C1101 " both_signs ideal model delta sigma weight residual False 2.49 -3.13 5.61 2.00e-01 2.50e+01 7.88e+02 chirality pdb=" CA LEU C 852 " pdb=" N LEU C 852 " pdb=" C LEU C 852 " pdb=" CB LEU C 852 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA ALA B 222 " pdb=" N ALA B 222 " pdb=" C ALA B 222 " pdb=" CB ALA B 222 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 3910 not shown) Planarity restraints: 4261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 233 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C THR C 233 " -0.059 2.00e-02 2.50e+03 pdb=" O THR C 233 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL C 234 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 926 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE B 926 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE B 926 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 927 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 852 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO C 853 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 853 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 853 " 0.049 5.00e-02 4.00e+02 ... (remaining 4258 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7095 2.81 - 3.34: 23315 3.34 - 3.86: 40601 3.86 - 4.38: 49790 4.38 - 4.90: 79622 Nonbonded interactions: 200423 Sorted by model distance: nonbonded pdb=" N LYS C 796 " pdb=" N GLY C 797 " model vdw 2.293 2.560 nonbonded pdb=" N GLN B 775 " pdb=" O GLN B 775 " model vdw 2.395 2.496 nonbonded pdb=" N ASN C 509 " pdb=" O ASN C 509 " model vdw 2.412 2.496 nonbonded pdb=" N GLY A 756 " pdb=" O GLY A 756 " model vdw 2.433 2.496 nonbonded pdb=" OG1 THR B 589 " pdb=" O GLN B 623 " model vdw 2.455 2.440 ... (remaining 200418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 1045) selection = chain 'B' selection = (chain 'C' and resid 1 through 1045) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 2.150 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 68.250 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.100 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.012 0.315 24442 Z= 0.807 Angle : 1.585 23.530 33247 Z= 1.073 Chirality : 0.144 5.614 3913 Planarity : 0.009 0.083 4261 Dihedral : 12.650 132.974 8799 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 3.21 % Allowed : 8.19 % Favored : 88.60 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3134 helix: 0.66 (0.12), residues: 1720 sheet: 0.86 (0.23), residues: 453 loop : -0.43 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 810 HIS 0.011 0.002 HIS C 424 PHE 0.022 0.002 PHE A 277 TYR 0.030 0.003 TYR A 327 ARG 0.008 0.001 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 720 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7513 (ttt) cc_final: 0.7286 (ttt) REVERT: A 58 GLU cc_start: 0.8051 (tt0) cc_final: 0.7549 (tt0) REVERT: A 64 ILE cc_start: 0.7830 (mm) cc_final: 0.7583 (OUTLIER) REVERT: A 66 GLU cc_start: 0.7033 (tt0) cc_final: 0.6577 (tt0) REVERT: A 68 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: A 87 GLN cc_start: 0.8316 (mt0) cc_final: 0.8037 (mt0) REVERT: A 99 ASP cc_start: 0.7750 (t70) cc_final: 0.7375 (t0) REVERT: A 101 ASP cc_start: 0.7885 (m-30) cc_final: 0.7675 (m-30) REVERT: A 128 THR cc_start: 0.8244 (m) cc_final: 0.7963 (p) REVERT: A 153 ASP cc_start: 0.7485 (m-30) cc_final: 0.7241 (m-30) REVERT: A 199 THR cc_start: 0.8256 (p) cc_final: 0.8014 (t) REVERT: A 244 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6404 (mp0) REVERT: A 252 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6771 (ptmt) REVERT: A 278 ASP cc_start: 0.7341 (t0) cc_final: 0.6969 (t0) REVERT: A 292 LYS cc_start: 0.6950 (mttt) cc_final: 0.6461 (mttm) REVERT: A 307 GLU cc_start: 0.6935 (tp30) cc_final: 0.6627 (tp30) REVERT: A 308 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6662 (tp-100) REVERT: A 338 GLU cc_start: 0.6873 (tt0) cc_final: 0.6665 (tt0) REVERT: A 339 SER cc_start: 0.8377 (t) cc_final: 0.7978 (p) REVERT: A 389 SER cc_start: 0.8518 (p) cc_final: 0.8315 (p) REVERT: A 525 MET cc_start: 0.5015 (tpt) cc_final: 0.4678 (tpt) REVERT: A 559 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7224 (mm-40) REVERT: A 601 MET cc_start: 0.8495 (mtm) cc_final: 0.8287 (mtp) REVERT: A 606 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8005 (t) REVERT: A 617 SER cc_start: 0.8139 (t) cc_final: 0.7924 (p) REVERT: A 633 LYS cc_start: 0.7520 (mttm) cc_final: 0.7241 (mttt) REVERT: A 673 MET cc_start: 0.6743 (mtt) cc_final: 0.6397 (mtm) REVERT: A 687 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: A 692 GLN cc_start: 0.7935 (mt0) cc_final: 0.7654 (mt0) REVERT: A 729 GLN cc_start: 0.7257 (tt0) cc_final: 0.6937 (tt0) REVERT: A 752 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6774 (ptt90) REVERT: A 765 ASP cc_start: 0.7361 (t0) cc_final: 0.6940 (t0) REVERT: A 777 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7037 (OUTLIER) REVERT: A 840 ASP cc_start: 0.7715 (m-30) cc_final: 0.7270 (m-30) REVERT: A 843 LYS cc_start: 0.7209 (mttt) cc_final: 0.6839 (mtpt) REVERT: A 857 LEU cc_start: 0.7688 (mm) cc_final: 0.7157 (mp) REVERT: A 884 LEU cc_start: 0.8056 (tp) cc_final: 0.7734 (mt) REVERT: A 904 PHE cc_start: 0.7201 (m-80) cc_final: 0.6975 (m-10) REVERT: A 955 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7877 (tp) REVERT: A 959 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: A 975 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 980 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6931 (ttmm) REVERT: A 988 MET cc_start: 0.7579 (ttm) cc_final: 0.7333 (mtp) REVERT: B 17 LEU cc_start: 0.7733 (mt) cc_final: 0.7458 (mt) REVERT: B 20 MET cc_start: 0.7621 (mtp) cc_final: 0.7263 (mtm) REVERT: B 66 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 79 SER cc_start: 0.8506 (t) cc_final: 0.8214 (p) REVERT: B 117 LEU cc_start: 0.8460 (mt) cc_final: 0.8204 (mt) REVERT: B 138 GLN cc_start: 0.8034 (pt0) cc_final: 0.7597 (mt0) REVERT: B 146 ASP cc_start: 0.7494 (m-30) cc_final: 0.7240 (m-30) REVERT: B 151 ASP cc_start: 0.5979 (p0) cc_final: 0.5635 (p0) REVERT: B 208 GLN cc_start: 0.7424 (mt0) cc_final: 0.7059 (mm-40) REVERT: B 252 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7064 (ptpt) REVERT: B 284 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7020 (tmmt) REVERT: B 325 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6693 (tp) REVERT: B 338 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6499 (tm-30) REVERT: B 395 MET cc_start: 0.7291 (mmm) cc_final: 0.7079 (tpp) REVERT: B 481 SER cc_start: 0.7581 (t) cc_final: 0.7236 (p) REVERT: B 574 VAL cc_start: 0.8257 (p) cc_final: 0.8005 (t) REVERT: B 575 MET cc_start: 0.7124 (ttp) cc_final: 0.6557 (ttp) REVERT: B 594 ASP cc_start: 0.6930 (m-30) cc_final: 0.6568 (m-30) REVERT: B 653 MET cc_start: 0.7571 (tpp) cc_final: 0.7268 (tpp) REVERT: B 687 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7689 (mtpp) REVERT: B 733 ASP cc_start: 0.6936 (t0) cc_final: 0.6584 (t0) REVERT: B 740 MET cc_start: 0.7253 (mtp) cc_final: 0.6977 (mtt) REVERT: B 742 VAL cc_start: 0.8471 (t) cc_final: 0.8150 (t) REVERT: B 818 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7475 (mp0) REVERT: B 849 ILE cc_start: 0.8772 (mt) cc_final: 0.8512 (mp) REVERT: C 30 MET cc_start: 0.8457 (ttp) cc_final: 0.8146 (ttt) REVERT: C 69 MET cc_start: 0.8290 (mmt) cc_final: 0.5621 (mmp) REVERT: C 95 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6644 (mm-30) REVERT: C 99 ASP cc_start: 0.7691 (t70) cc_final: 0.7441 (t0) REVERT: C 110 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7720 (mmtm) REVERT: C 120 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6533 (tm-30) REVERT: C 130 THR cc_start: 0.8726 (p) cc_final: 0.8448 (t) REVERT: C 136 PHE cc_start: 0.7304 (m-80) cc_final: 0.7060 (m-10) REVERT: C 140 ILE cc_start: 0.8218 (mt) cc_final: 0.7883 (mp) REVERT: C 174 GLU cc_start: 0.7188 (tt0) cc_final: 0.5900 (tp30) REVERT: C 218 GLN cc_start: 0.8448 (mt0) cc_final: 0.8047 (mt0) REVERT: C 284 LYS cc_start: 0.5851 (mmtp) cc_final: 0.5647 (mtpp) REVERT: C 293 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7082 (mm) REVERT: C 314 ARG cc_start: 0.6078 (mtm-85) cc_final: 0.5854 (mtm180) REVERT: C 324 LYS cc_start: 0.6332 (ttpp) cc_final: 0.5713 (mtpt) REVERT: C 363 ARG cc_start: 0.7647 (mmt90) cc_final: 0.7348 (mtt180) REVERT: C 423 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6002 (p0) REVERT: C 463 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7568 (m) REVERT: C 499 GLN cc_start: 0.7357 (tt0) cc_final: 0.7053 (tm-30) REVERT: C 587 ASP cc_start: 0.5873 (m-30) cc_final: 0.5489 (t0) REVERT: C 599 PHE cc_start: 0.6281 (t80) cc_final: 0.5867 (t80) REVERT: C 603 GLU cc_start: 0.5814 (mm-30) cc_final: 0.4967 (mm-30) REVERT: C 633 LYS cc_start: 0.6125 (mttm) cc_final: 0.5892 (mtmm) REVERT: C 666 MET cc_start: 0.6163 (ttm) cc_final: 0.5264 (tpp) REVERT: C 687 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7464 (mtpt) REVERT: C 729 GLN cc_start: 0.7158 (tt0) cc_final: 0.6941 (tt0) REVERT: C 768 ARG cc_start: 0.6372 (mmt180) cc_final: 0.5749 (mmm160) REVERT: C 771 LYS cc_start: 0.8215 (mttm) cc_final: 0.7589 (mtpp) REVERT: C 789 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7263 (mttt) REVERT: C 809 GLU cc_start: 0.7284 (pt0) cc_final: 0.6920 (pt0) REVERT: C 845 MET cc_start: 0.7303 (mmm) cc_final: 0.7054 (mmm) REVERT: C 863 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 873 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5913 (mt-10) REVERT: C 904 PHE cc_start: 0.7950 (m-80) cc_final: 0.7402 (m-80) REVERT: C 911 PRO cc_start: 0.7994 (Cg_exo) cc_final: 0.7727 (Cg_endo) REVERT: C 912 LEU cc_start: 0.7808 (mt) cc_final: 0.7523 (mp) REVERT: C 932 ASN cc_start: 0.7695 (m-40) cc_final: 0.7441 (m-40) REVERT: C 937 ILE cc_start: 0.7812 (pp) cc_final: 0.7521 (mt) REVERT: C 1038 VAL cc_start: 0.7656 (t) cc_final: 0.7318 (m) outliers start: 83 outliers final: 21 residues processed: 775 average time/residue: 1.0736 time to fit residues: 985.1419 Evaluate side-chains 607 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 575 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 688 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 108 GLN A 125 GLN A 231 ASN A 274 ASN A 298 ASN A 531 ASN A 669 GLN B 87 GLN B 108 GLN B 391 ASN B 415 ASN B 729 GLN B 731 ASN C 123 GLN C 125 GLN C 138 GLN C 274 ASN C 531 ASN C 795 ASN C 829 GLN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24442 Z= 0.238 Angle : 0.677 24.767 33247 Z= 0.340 Chirality : 0.054 2.021 3913 Planarity : 0.006 0.062 4261 Dihedral : 7.016 112.907 3404 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.37 % Allowed : 15.46 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3134 helix: 1.59 (0.12), residues: 1707 sheet: 0.85 (0.24), residues: 422 loop : -0.09 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 362 HIS 0.006 0.001 HIS A1012 PHE 0.025 0.002 PHE B 993 TYR 0.018 0.002 TYR B 157 ARG 0.007 0.001 ARG C 433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 612 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7060 (tt0) cc_final: 0.6553 (mt-10) REVERT: A 69 MET cc_start: 0.8468 (mmt) cc_final: 0.7969 (mmt) REVERT: A 87 GLN cc_start: 0.8301 (mt0) cc_final: 0.8041 (mt0) REVERT: A 99 ASP cc_start: 0.7754 (t70) cc_final: 0.7369 (t0) REVERT: A 128 THR cc_start: 0.8207 (m) cc_final: 0.7950 (p) REVERT: A 153 ASP cc_start: 0.7347 (m-30) cc_final: 0.7118 (m-30) REVERT: A 208 GLN cc_start: 0.7694 (mm110) cc_final: 0.7036 (mm110) REVERT: A 252 LYS cc_start: 0.7124 (ttpt) cc_final: 0.6779 (ttmt) REVERT: A 278 ASP cc_start: 0.7337 (t0) cc_final: 0.7095 (t0) REVERT: A 292 LYS cc_start: 0.6850 (mttt) cc_final: 0.6415 (mttm) REVERT: A 307 GLU cc_start: 0.7012 (tp30) cc_final: 0.6545 (tp30) REVERT: A 338 GLU cc_start: 0.6694 (tt0) cc_final: 0.5948 (tp30) REVERT: A 420 MET cc_start: 0.8038 (mtp) cc_final: 0.7655 (mtp) REVERT: A 438 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6366 (mp) REVERT: A 447 SER cc_start: 0.8728 (m) cc_final: 0.8521 (m) REVERT: A 525 MET cc_start: 0.4434 (tpt) cc_final: 0.4072 (tpt) REVERT: A 559 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7307 (mm110) REVERT: A 564 SER cc_start: 0.8386 (t) cc_final: 0.8182 (p) REVERT: A 568 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: A 602 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7223 (m-40) REVERT: A 617 SER cc_start: 0.8179 (t) cc_final: 0.7952 (p) REVERT: A 637 LYS cc_start: 0.7408 (mmmt) cc_final: 0.7109 (mmmm) REVERT: A 673 MET cc_start: 0.6578 (mtt) cc_final: 0.6142 (mtm) REVERT: A 727 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5923 (mt0) REVERT: A 729 GLN cc_start: 0.7062 (tt0) cc_final: 0.6733 (tt0) REVERT: A 752 ARG cc_start: 0.7102 (ttp80) cc_final: 0.6887 (ptt90) REVERT: A 759 TYR cc_start: 0.7877 (t80) cc_final: 0.7604 (t80) REVERT: A 762 ASP cc_start: 0.7946 (m-30) cc_final: 0.7150 (m-30) REVERT: A 765 ASP cc_start: 0.7461 (t0) cc_final: 0.6977 (t0) REVERT: A 777 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: A 840 ASP cc_start: 0.7643 (m-30) cc_final: 0.7280 (m-30) REVERT: A 843 LYS cc_start: 0.7023 (mttt) cc_final: 0.6534 (mtpt) REVERT: A 855 MET cc_start: 0.7879 (mtm) cc_final: 0.7647 (mtp) REVERT: A 884 LEU cc_start: 0.8028 (tp) cc_final: 0.7690 (mt) REVERT: A 904 PHE cc_start: 0.7305 (m-80) cc_final: 0.6970 (m-10) REVERT: A 930 ASP cc_start: 0.7406 (t0) cc_final: 0.7204 (t0) REVERT: A 955 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 980 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6876 (ttmm) REVERT: A 983 LEU cc_start: 0.7960 (tp) cc_final: 0.7709 (tm) REVERT: B 8 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6706 (mtt180) REVERT: B 17 LEU cc_start: 0.7779 (mt) cc_final: 0.7452 (mt) REVERT: B 20 MET cc_start: 0.7563 (mtp) cc_final: 0.7210 (mtm) REVERT: B 66 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 151 ASP cc_start: 0.5950 (p0) cc_final: 0.5620 (p0) REVERT: B 184 MET cc_start: 0.8810 (mmt) cc_final: 0.8128 (tpp) REVERT: B 247 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7816 (mtpt) REVERT: B 263 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7475 (pttt) REVERT: B 267 ARG cc_start: 0.7925 (ttt-90) cc_final: 0.7716 (ttt180) REVERT: B 284 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6909 (tmmt) REVERT: B 325 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6911 (tp) REVERT: B 338 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6452 (tm-30) REVERT: B 395 MET cc_start: 0.7186 (mmm) cc_final: 0.6956 (mmm) REVERT: B 420 MET cc_start: 0.7850 (ttp) cc_final: 0.7597 (ttt) REVERT: B 481 SER cc_start: 0.7676 (t) cc_final: 0.7267 (p) REVERT: B 574 VAL cc_start: 0.8166 (p) cc_final: 0.7914 (t) REVERT: B 575 MET cc_start: 0.7292 (ttp) cc_final: 0.6418 (ttp) REVERT: B 594 ASP cc_start: 0.6820 (m-30) cc_final: 0.6562 (m-30) REVERT: B 609 SER cc_start: 0.7055 (OUTLIER) cc_final: 0.6807 (p) REVERT: B 653 MET cc_start: 0.7245 (tpp) cc_final: 0.7024 (tpp) REVERT: B 687 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7845 (mtpp) REVERT: B 733 ASP cc_start: 0.6981 (t0) cc_final: 0.6657 (t0) REVERT: B 740 MET cc_start: 0.7176 (mtp) cc_final: 0.6609 (mtt) REVERT: B 818 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 848 ILE cc_start: 0.8732 (mt) cc_final: 0.8501 (mt) REVERT: B 849 ILE cc_start: 0.8648 (mt) cc_final: 0.8405 (mp) REVERT: B 863 GLU cc_start: 0.7071 (tt0) cc_final: 0.6699 (tt0) REVERT: B 892 CYS cc_start: 0.8136 (m) cc_final: 0.7352 (m) REVERT: B 925 MET cc_start: 0.7825 (tmt) cc_final: 0.7522 (tmm) REVERT: B 981 MET cc_start: 0.8559 (ttp) cc_final: 0.8354 (tpp) REVERT: B 987 ILE cc_start: 0.7558 (mm) cc_final: 0.7318 (mp) REVERT: B 988 MET cc_start: 0.7745 (ptm) cc_final: 0.7171 (mtm) REVERT: C 8 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7102 (mtm-85) REVERT: C 20 MET cc_start: 0.6532 (mtp) cc_final: 0.6026 (mtm) REVERT: C 30 MET cc_start: 0.8353 (ttp) cc_final: 0.8141 (ttt) REVERT: C 64 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8139 (mp) REVERT: C 69 MET cc_start: 0.8139 (mmt) cc_final: 0.5462 (mmp) REVERT: C 95 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6869 (mm-30) REVERT: C 99 ASP cc_start: 0.7610 (t70) cc_final: 0.7342 (t0) REVERT: C 120 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6638 (tm-30) REVERT: C 130 THR cc_start: 0.8639 (p) cc_final: 0.8335 (t) REVERT: C 136 PHE cc_start: 0.7518 (m-80) cc_final: 0.7096 (m-10) REVERT: C 137 LEU cc_start: 0.7838 (tp) cc_final: 0.7635 (tt) REVERT: C 140 ILE cc_start: 0.8235 (mt) cc_final: 0.7888 (mp) REVERT: C 168 ARG cc_start: 0.7013 (mtt90) cc_final: 0.6803 (mtt90) REVERT: C 202 ASP cc_start: 0.8063 (m-30) cc_final: 0.7816 (m-30) REVERT: C 218 GLN cc_start: 0.8566 (mt0) cc_final: 0.8065 (mt0) REVERT: C 284 LYS cc_start: 0.5837 (mmtp) cc_final: 0.5541 (mtpp) REVERT: C 324 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5769 (mttm) REVERT: C 417 GLU cc_start: 0.7428 (tp30) cc_final: 0.7228 (tp30) REVERT: C 422 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6441 (mt-10) REVERT: C 459 PHE cc_start: 0.7235 (m-80) cc_final: 0.6979 (m-80) REVERT: C 468 ARG cc_start: 0.7425 (ttm110) cc_final: 0.6918 (ttp-110) REVERT: C 499 GLN cc_start: 0.7074 (tt0) cc_final: 0.6815 (tm-30) REVERT: C 530 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6422 (mm-40) REVERT: C 536 MET cc_start: 0.7305 (mmm) cc_final: 0.6799 (mtt) REVERT: C 575 MET cc_start: 0.6692 (ttm) cc_final: 0.6336 (ttm) REVERT: C 599 PHE cc_start: 0.6184 (t80) cc_final: 0.5852 (t80) REVERT: C 603 GLU cc_start: 0.5515 (mm-30) cc_final: 0.4708 (mm-30) REVERT: C 666 MET cc_start: 0.5572 (ttm) cc_final: 0.4732 (tpp) REVERT: C 668 LEU cc_start: 0.6315 (mt) cc_final: 0.5981 (mp) REVERT: C 683 ASN cc_start: 0.7659 (t0) cc_final: 0.7060 (t0) REVERT: C 687 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: C 729 GLN cc_start: 0.7273 (tt0) cc_final: 0.6391 (tp-100) REVERT: C 751 MET cc_start: 0.8019 (mtm) cc_final: 0.7731 (mtm) REVERT: C 768 ARG cc_start: 0.6292 (mmt180) cc_final: 0.5632 (mtp180) REVERT: C 842 MET cc_start: 0.7141 (mtt) cc_final: 0.6928 (mtp) REVERT: C 845 MET cc_start: 0.7440 (mmm) cc_final: 0.7040 (mmt) REVERT: C 873 GLU cc_start: 0.5890 (mt-10) cc_final: 0.5626 (mt-10) REVERT: C 887 LEU cc_start: 0.7188 (tp) cc_final: 0.6814 (tm) REVERT: C 904 PHE cc_start: 0.7947 (m-80) cc_final: 0.7346 (m-80) REVERT: C 932 ASN cc_start: 0.7615 (m-40) cc_final: 0.7382 (m-40) REVERT: C 940 GLN cc_start: 0.7407 (mt0) cc_final: 0.7075 (mt0) REVERT: C 943 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 982 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7988 (mmm160) REVERT: C 1012 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7634 (m170) REVERT: C 1023 LEU cc_start: 0.7973 (mt) cc_final: 0.7771 (mm) REVERT: C 1045 LYS cc_start: 0.7272 (mtpt) cc_final: 0.7058 (ttmm) outliers start: 113 outliers final: 37 residues processed: 677 average time/residue: 1.0995 time to fit residues: 880.1000 Evaluate side-chains 601 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 549 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 997 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 777 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1012 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 63 GLN A 316 ASN A 749 ASN A 977 HIS B 87 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 148 ASN C 274 ASN C 531 ASN C 579 GLN C 731 ASN C 795 ASN C 829 GLN C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 24442 Z= 0.437 Angle : 0.742 23.845 33247 Z= 0.375 Chirality : 0.058 2.043 3913 Planarity : 0.006 0.056 4261 Dihedral : 6.731 108.696 3370 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.56 % Allowed : 15.92 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3134 helix: 1.51 (0.12), residues: 1700 sheet: 0.51 (0.24), residues: 434 loop : -0.21 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 790 HIS 0.010 0.001 HIS C 424 PHE 0.022 0.002 PHE C 860 TYR 0.028 0.003 TYR A 327 ARG 0.008 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 563 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6769 (mm-40) REVERT: A 66 GLU cc_start: 0.7374 (tt0) cc_final: 0.6929 (tt0) REVERT: A 69 MET cc_start: 0.8523 (mmt) cc_final: 0.8091 (mmt) REVERT: A 95 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 99 ASP cc_start: 0.7844 (t70) cc_final: 0.7451 (t0) REVERT: A 128 THR cc_start: 0.8243 (m) cc_final: 0.7952 (p) REVERT: A 153 ASP cc_start: 0.7343 (m-30) cc_final: 0.7089 (m-30) REVERT: A 208 GLN cc_start: 0.7762 (mm110) cc_final: 0.7111 (mm110) REVERT: A 252 LYS cc_start: 0.7344 (ttpt) cc_final: 0.7018 (ttmt) REVERT: A 278 ASP cc_start: 0.7403 (t0) cc_final: 0.7144 (t0) REVERT: A 292 LYS cc_start: 0.6946 (mttt) cc_final: 0.6488 (mttm) REVERT: A 307 GLU cc_start: 0.7110 (tp30) cc_final: 0.6696 (tp30) REVERT: A 338 GLU cc_start: 0.6657 (tt0) cc_final: 0.6194 (tp30) REVERT: A 342 HIS cc_start: 0.6856 (t70) cc_final: 0.6441 (t-170) REVERT: A 402 ILE cc_start: 0.8290 (mm) cc_final: 0.8069 (mt) REVERT: A 438 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6814 (mm) REVERT: A 525 MET cc_start: 0.4584 (tpt) cc_final: 0.4212 (tpt) REVERT: A 554 LEU cc_start: 0.8084 (tt) cc_final: 0.7731 (tp) REVERT: A 559 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7185 (mm110) REVERT: A 568 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: A 602 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: A 637 LYS cc_start: 0.7509 (mmmt) cc_final: 0.7194 (mmmt) REVERT: A 657 MET cc_start: 0.6243 (mmm) cc_final: 0.6022 (mmp) REVERT: A 669 GLN cc_start: 0.7506 (mt0) cc_final: 0.7050 (mt0) REVERT: A 673 MET cc_start: 0.6619 (mtt) cc_final: 0.6216 (mtm) REVERT: A 718 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7922 (ptt-90) REVERT: A 722 GLN cc_start: 0.7056 (mt0) cc_final: 0.6825 (mt0) REVERT: A 729 GLN cc_start: 0.7258 (tt0) cc_final: 0.6870 (tt0) REVERT: A 752 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6893 (ptt90) REVERT: A 759 TYR cc_start: 0.8155 (t80) cc_final: 0.7797 (t80) REVERT: A 777 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: A 783 MET cc_start: 0.6152 (mmm) cc_final: 0.5913 (mmm) REVERT: A 816 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7067 (ttp-110) REVERT: A 840 ASP cc_start: 0.7719 (m-30) cc_final: 0.7354 (m-30) REVERT: A 843 LYS cc_start: 0.7223 (mttt) cc_final: 0.6902 (mtpm) REVERT: A 884 LEU cc_start: 0.8144 (tp) cc_final: 0.7728 (mt) REVERT: A 904 PHE cc_start: 0.7243 (m-80) cc_final: 0.6944 (m-10) REVERT: A 955 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 980 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6947 (ttmm) REVERT: A 983 LEU cc_start: 0.7985 (tp) cc_final: 0.7710 (tm) REVERT: B 8 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6636 (mtt180) REVERT: B 17 LEU cc_start: 0.7844 (mt) cc_final: 0.7624 (mt) REVERT: B 20 MET cc_start: 0.7727 (mtp) cc_final: 0.7416 (mtm) REVERT: B 66 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 67 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: B 151 ASP cc_start: 0.6039 (p0) cc_final: 0.5734 (p0) REVERT: B 184 MET cc_start: 0.8866 (mmt) cc_final: 0.7829 (tpp) REVERT: B 263 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7457 (pttt) REVERT: B 284 LYS cc_start: 0.7701 (mtmt) cc_final: 0.6932 (tmmt) REVERT: B 323 ASP cc_start: 0.7249 (p0) cc_final: 0.7039 (p0) REVERT: B 338 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6568 (tm-30) REVERT: B 395 MET cc_start: 0.7257 (mmm) cc_final: 0.6998 (tpp) REVERT: B 398 MET cc_start: 0.7048 (tpt) cc_final: 0.6664 (mmt) REVERT: B 420 MET cc_start: 0.7961 (ttp) cc_final: 0.7456 (ttt) REVERT: B 481 SER cc_start: 0.7578 (t) cc_final: 0.7157 (p) REVERT: B 575 MET cc_start: 0.7299 (ttp) cc_final: 0.6445 (ttp) REVERT: B 594 ASP cc_start: 0.6685 (m-30) cc_final: 0.6394 (m-30) REVERT: B 609 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6820 (p) REVERT: B 653 MET cc_start: 0.7219 (tpp) cc_final: 0.6972 (tpp) REVERT: B 657 MET cc_start: 0.7042 (ttp) cc_final: 0.6779 (tmm) REVERT: B 687 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7711 (mtpp) REVERT: B 698 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6996 (mp) REVERT: B 730 ILE cc_start: 0.8179 (mt) cc_final: 0.7870 (mm) REVERT: B 733 ASP cc_start: 0.7054 (t0) cc_final: 0.6605 (t0) REVERT: B 736 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.5705 (mm110) REVERT: B 740 MET cc_start: 0.7110 (mtp) cc_final: 0.6564 (mtt) REVERT: B 818 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 845 MET cc_start: 0.7618 (mmm) cc_final: 0.7145 (mmt) REVERT: B 849 ILE cc_start: 0.8628 (mt) cc_final: 0.8340 (mp) REVERT: B 891 LEU cc_start: 0.7018 (mt) cc_final: 0.6683 (mm) REVERT: B 892 CYS cc_start: 0.8151 (m) cc_final: 0.7369 (m) REVERT: B 925 MET cc_start: 0.7790 (tmt) cc_final: 0.7540 (tmm) REVERT: B 987 ILE cc_start: 0.7578 (mm) cc_final: 0.7351 (OUTLIER) REVERT: C 8 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7115 (mtm-85) REVERT: C 20 MET cc_start: 0.6589 (mtp) cc_final: 0.6042 (mtm) REVERT: C 30 MET cc_start: 0.8294 (ttp) cc_final: 0.8045 (ttt) REVERT: C 69 MET cc_start: 0.8089 (mmt) cc_final: 0.5579 (mmp) REVERT: C 95 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6913 (mm-30) REVERT: C 99 ASP cc_start: 0.7639 (t70) cc_final: 0.7370 (t0) REVERT: C 120 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6521 (tm-30) REVERT: C 140 ILE cc_start: 0.8221 (mt) cc_final: 0.7862 (mp) REVERT: C 405 LEU cc_start: 0.7476 (mp) cc_final: 0.7234 (mm) REVERT: C 417 GLU cc_start: 0.7641 (tp30) cc_final: 0.7395 (tp30) REVERT: C 422 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6567 (mt-10) REVERT: C 423 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5694 (p0) REVERT: C 433 ARG cc_start: 0.7286 (ttt90) cc_final: 0.6861 (ttt-90) REVERT: C 462 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7332 (t) REVERT: C 468 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7157 (mtm-85) REVERT: C 499 GLN cc_start: 0.7313 (tt0) cc_final: 0.7000 (tm-30) REVERT: C 530 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: C 536 MET cc_start: 0.7291 (mmm) cc_final: 0.6971 (mtt) REVERT: C 575 MET cc_start: 0.6819 (ttm) cc_final: 0.6354 (ttm) REVERT: C 591 LYS cc_start: 0.5130 (mttt) cc_final: 0.4893 (mtpt) REVERT: C 599 PHE cc_start: 0.6264 (t80) cc_final: 0.6049 (t80) REVERT: C 666 MET cc_start: 0.5616 (ttm) cc_final: 0.4705 (tpp) REVERT: C 668 LEU cc_start: 0.6331 (mt) cc_final: 0.5964 (mp) REVERT: C 696 LYS cc_start: 0.7041 (mmmt) cc_final: 0.6602 (tppp) REVERT: C 705 LEU cc_start: 0.7978 (mt) cc_final: 0.7686 (mt) REVERT: C 707 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7641 (mp) REVERT: C 729 GLN cc_start: 0.7008 (tt0) cc_final: 0.6433 (tp-100) REVERT: C 768 ARG cc_start: 0.6500 (mmt180) cc_final: 0.5743 (mtp180) REVERT: C 800 VAL cc_start: 0.7733 (t) cc_final: 0.7242 (m) REVERT: C 842 MET cc_start: 0.7194 (mtt) cc_final: 0.6907 (mtp) REVERT: C 857 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6814 (mp) REVERT: C 873 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5172 (mt-10) REVERT: C 887 LEU cc_start: 0.7404 (tp) cc_final: 0.6956 (tm) REVERT: C 904 PHE cc_start: 0.7639 (m-80) cc_final: 0.7160 (m-80) REVERT: C 932 ASN cc_start: 0.7681 (m-40) cc_final: 0.7472 (m-40) REVERT: C 937 ILE cc_start: 0.7567 (pp) cc_final: 0.7367 (mt) REVERT: C 940 GLN cc_start: 0.7545 (mt0) cc_final: 0.7216 (mt0) REVERT: C 943 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7804 (mm) REVERT: C 963 GLU cc_start: 0.6548 (tt0) cc_final: 0.5931 (mm-30) REVERT: C 1023 LEU cc_start: 0.7965 (mt) cc_final: 0.7683 (mm) outliers start: 144 outliers final: 68 residues processed: 644 average time/residue: 1.0887 time to fit residues: 832.5750 Evaluate side-chains 631 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 546 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 782 MET Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 698 ILE Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 614 SER Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 851 LYS Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 125 GLN A 241 GLN A 669 GLN A 749 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 148 ASN C 274 ASN C 731 ASN C 795 ASN C 829 GLN C 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24442 Z= 0.227 Angle : 0.624 23.438 33247 Z= 0.302 Chirality : 0.053 2.028 3913 Planarity : 0.005 0.052 4261 Dihedral : 6.200 105.325 3359 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.48 % Allowed : 18.20 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3134 helix: 1.98 (0.12), residues: 1693 sheet: 0.45 (0.24), residues: 445 loop : -0.07 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 755 HIS 0.004 0.001 HIS C 424 PHE 0.020 0.001 PHE C 939 TYR 0.017 0.001 TYR A 664 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 566 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8568 (mmt) cc_final: 0.8018 (mmt) REVERT: A 99 ASP cc_start: 0.7833 (t70) cc_final: 0.7414 (t0) REVERT: A 117 LEU cc_start: 0.8276 (mt) cc_final: 0.8047 (mm) REVERT: A 128 THR cc_start: 0.8212 (m) cc_final: 0.7969 (p) REVERT: A 138 GLN cc_start: 0.7772 (mt0) cc_final: 0.7560 (mt0) REVERT: A 153 ASP cc_start: 0.7299 (m-30) cc_final: 0.7052 (m-30) REVERT: A 208 GLN cc_start: 0.7725 (mm110) cc_final: 0.6997 (mm110) REVERT: A 252 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6906 (ttmt) REVERT: A 261 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6807 (mtt-85) REVERT: A 269 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: A 278 ASP cc_start: 0.7373 (t0) cc_final: 0.7141 (t0) REVERT: A 292 LYS cc_start: 0.6860 (mttt) cc_final: 0.6430 (mttm) REVERT: A 307 GLU cc_start: 0.7066 (tp30) cc_final: 0.6644 (tp30) REVERT: A 342 HIS cc_start: 0.6827 (t70) cc_final: 0.6388 (t-170) REVERT: A 438 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6426 (mp) REVERT: A 447 SER cc_start: 0.8763 (m) cc_final: 0.8494 (m) REVERT: A 525 MET cc_start: 0.4433 (tpt) cc_final: 0.4130 (tpt) REVERT: A 559 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7158 (mm110) REVERT: A 568 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: A 602 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7217 (m-40) REVERT: A 633 LYS cc_start: 0.7584 (mttm) cc_final: 0.7309 (mttt) REVERT: A 637 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7327 (mmmm) REVERT: A 657 MET cc_start: 0.6189 (mmm) cc_final: 0.5971 (mmp) REVERT: A 669 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: A 673 MET cc_start: 0.6711 (mtt) cc_final: 0.6362 (mtm) REVERT: A 695 GLU cc_start: 0.7432 (mp0) cc_final: 0.7017 (mp0) REVERT: A 722 GLN cc_start: 0.6990 (mt0) cc_final: 0.6762 (mt0) REVERT: A 729 GLN cc_start: 0.7051 (tt0) cc_final: 0.6721 (tt0) REVERT: A 752 ARG cc_start: 0.7073 (ttp80) cc_final: 0.6841 (ptt90) REVERT: A 759 TYR cc_start: 0.7988 (t80) cc_final: 0.7654 (t80) REVERT: A 783 MET cc_start: 0.6108 (mmm) cc_final: 0.5811 (mmm) REVERT: A 816 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7174 (ttp-110) REVERT: A 840 ASP cc_start: 0.7645 (m-30) cc_final: 0.7271 (m-30) REVERT: A 843 LYS cc_start: 0.7158 (mttt) cc_final: 0.6855 (mtpm) REVERT: A 884 LEU cc_start: 0.8112 (tp) cc_final: 0.7699 (mt) REVERT: A 904 PHE cc_start: 0.7233 (m-80) cc_final: 0.7005 (m-10) REVERT: A 955 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 980 LYS cc_start: 0.7166 (ttmt) cc_final: 0.6879 (ttmm) REVERT: A 983 LEU cc_start: 0.7908 (tp) cc_final: 0.7677 (tm) REVERT: B 8 ARG cc_start: 0.6837 (mpt180) cc_final: 0.6602 (mtt90) REVERT: B 17 LEU cc_start: 0.7869 (mt) cc_final: 0.7497 (mt) REVERT: B 20 MET cc_start: 0.7621 (mtp) cc_final: 0.7292 (mtm) REVERT: B 58 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: B 66 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7563 (mt-10) REVERT: B 151 ASP cc_start: 0.5959 (p0) cc_final: 0.5615 (p0) REVERT: B 184 MET cc_start: 0.8807 (mmt) cc_final: 0.7576 (tpp) REVERT: B 263 LYS cc_start: 0.7912 (ptpt) cc_final: 0.7416 (pttt) REVERT: B 284 LYS cc_start: 0.7708 (mtmt) cc_final: 0.6959 (tmmt) REVERT: B 338 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6504 (mm-30) REVERT: B 386 PHE cc_start: 0.7653 (m-10) cc_final: 0.7400 (m-80) REVERT: B 395 MET cc_start: 0.7277 (mmm) cc_final: 0.7037 (mmm) REVERT: B 398 MET cc_start: 0.7081 (tpt) cc_final: 0.6664 (mmt) REVERT: B 420 MET cc_start: 0.7899 (ttp) cc_final: 0.7485 (ttt) REVERT: B 481 SER cc_start: 0.7582 (t) cc_final: 0.7190 (p) REVERT: B 575 MET cc_start: 0.7376 (ttp) cc_final: 0.6300 (tpp) REVERT: B 594 ASP cc_start: 0.6718 (m-30) cc_final: 0.6341 (m-30) REVERT: B 609 SER cc_start: 0.7064 (OUTLIER) cc_final: 0.6854 (p) REVERT: B 653 MET cc_start: 0.7110 (tpp) cc_final: 0.6849 (tpp) REVERT: B 730 ILE cc_start: 0.8203 (mt) cc_final: 0.7886 (mm) REVERT: B 733 ASP cc_start: 0.7045 (t0) cc_final: 0.6547 (t0) REVERT: B 736 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5757 (mm110) REVERT: B 740 MET cc_start: 0.7115 (mtp) cc_final: 0.6606 (mtt) REVERT: B 845 MET cc_start: 0.7636 (mmm) cc_final: 0.7172 (mmt) REVERT: B 849 ILE cc_start: 0.8564 (mt) cc_final: 0.8288 (mp) REVERT: B 863 GLU cc_start: 0.7338 (tt0) cc_final: 0.6845 (mt-10) REVERT: B 891 LEU cc_start: 0.7012 (mt) cc_final: 0.6678 (mm) REVERT: B 892 CYS cc_start: 0.8104 (m) cc_final: 0.7299 (m) REVERT: B 987 ILE cc_start: 0.7557 (mm) cc_final: 0.7342 (OUTLIER) REVERT: C 8 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7141 (mtm-85) REVERT: C 17 LEU cc_start: 0.8279 (mp) cc_final: 0.8044 (mp) REVERT: C 20 MET cc_start: 0.6560 (mtp) cc_final: 0.6040 (mtm) REVERT: C 30 MET cc_start: 0.8284 (ttp) cc_final: 0.8060 (ttt) REVERT: C 38 ILE cc_start: 0.8373 (mm) cc_final: 0.7993 (pp) REVERT: C 95 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6967 (mm-30) REVERT: C 99 ASP cc_start: 0.7520 (t70) cc_final: 0.7303 (t0) REVERT: C 117 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8137 (mm) REVERT: C 120 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6701 (tm-30) REVERT: C 140 ILE cc_start: 0.8162 (mt) cc_final: 0.7857 (mp) REVERT: C 202 ASP cc_start: 0.8194 (m-30) cc_final: 0.7857 (m-30) REVERT: C 395 MET cc_start: 0.7498 (mmp) cc_final: 0.7260 (mmm) REVERT: C 405 LEU cc_start: 0.7427 (mp) cc_final: 0.7200 (mm) REVERT: C 417 GLU cc_start: 0.7593 (tp30) cc_final: 0.7373 (tp30) REVERT: C 422 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6175 (mt-10) REVERT: C 423 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5619 (p0) REVERT: C 462 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7349 (t) REVERT: C 468 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7134 (ttm-80) REVERT: C 499 GLN cc_start: 0.7157 (tt0) cc_final: 0.6882 (tm-30) REVERT: C 530 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6425 (mm-40) REVERT: C 536 MET cc_start: 0.7209 (mmm) cc_final: 0.6944 (mtt) REVERT: C 575 MET cc_start: 0.6711 (ttm) cc_final: 0.6227 (ttm) REVERT: C 591 LYS cc_start: 0.5134 (mttt) cc_final: 0.4862 (mtpt) REVERT: C 594 ASP cc_start: 0.4551 (t70) cc_final: 0.4228 (t70) REVERT: C 666 MET cc_start: 0.5616 (ttm) cc_final: 0.4698 (tpp) REVERT: C 668 LEU cc_start: 0.6320 (mt) cc_final: 0.5916 (mp) REVERT: C 705 LEU cc_start: 0.7898 (mt) cc_final: 0.7662 (mt) REVERT: C 707 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7627 (mp) REVERT: C 729 GLN cc_start: 0.7119 (tt0) cc_final: 0.6487 (tp-100) REVERT: C 768 ARG cc_start: 0.6643 (mmt180) cc_final: 0.5842 (mtp180) REVERT: C 800 VAL cc_start: 0.7732 (t) cc_final: 0.7253 (m) REVERT: C 842 MET cc_start: 0.7183 (mtt) cc_final: 0.6907 (mtp) REVERT: C 857 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6828 (mp) REVERT: C 861 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6372 (p0) REVERT: C 873 GLU cc_start: 0.5558 (mt-10) cc_final: 0.5083 (mt-10) REVERT: C 887 LEU cc_start: 0.7292 (tp) cc_final: 0.6870 (tm) REVERT: C 904 PHE cc_start: 0.7792 (m-80) cc_final: 0.7242 (m-80) REVERT: C 932 ASN cc_start: 0.7703 (m-40) cc_final: 0.7487 (m-40) REVERT: C 940 GLN cc_start: 0.7387 (mt0) cc_final: 0.7009 (mt0) REVERT: C 943 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7735 (mm) REVERT: C 963 GLU cc_start: 0.6582 (tt0) cc_final: 0.5882 (mm-30) REVERT: C 1023 LEU cc_start: 0.7971 (mt) cc_final: 0.7747 (mm) outliers start: 116 outliers final: 54 residues processed: 631 average time/residue: 1.0687 time to fit residues: 804.1211 Evaluate side-chains 616 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 543 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 176 GLN A 241 GLN A 749 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 148 ASN C 274 ASN C 531 ASN C 583 ASN C 598 ASN C 795 ASN C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24442 Z= 0.231 Angle : 0.625 23.484 33247 Z= 0.300 Chirality : 0.053 2.021 3913 Planarity : 0.004 0.052 4261 Dihedral : 6.034 104.170 3357 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.44 % Allowed : 18.43 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.15), residues: 3134 helix: 2.10 (0.12), residues: 1693 sheet: 0.44 (0.24), residues: 445 loop : -0.06 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 755 HIS 0.005 0.001 HIS C 424 PHE 0.026 0.001 PHE C 599 TYR 0.017 0.001 TYR A 327 ARG 0.004 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 550 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8054 (mt) cc_final: 0.7852 (mt) REVERT: A 66 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: A 69 MET cc_start: 0.8552 (mmt) cc_final: 0.8003 (mmt) REVERT: A 81 ASN cc_start: 0.7074 (m-40) cc_final: 0.6734 (m-40) REVERT: A 99 ASP cc_start: 0.7827 (t70) cc_final: 0.7398 (t0) REVERT: A 117 LEU cc_start: 0.8289 (mt) cc_final: 0.8064 (mm) REVERT: A 128 THR cc_start: 0.8218 (m) cc_final: 0.8008 (p) REVERT: A 153 ASP cc_start: 0.7260 (m-30) cc_final: 0.7043 (m-30) REVERT: A 208 GLN cc_start: 0.7657 (mm110) cc_final: 0.6957 (mm110) REVERT: A 252 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6916 (ttmt) REVERT: A 269 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: A 278 ASP cc_start: 0.7416 (t0) cc_final: 0.7187 (t0) REVERT: A 292 LYS cc_start: 0.6916 (mttt) cc_final: 0.6447 (mttm) REVERT: A 304 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6510 (pp20) REVERT: A 307 GLU cc_start: 0.7043 (tp30) cc_final: 0.6661 (tp30) REVERT: A 438 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6488 (mp) REVERT: A 447 SER cc_start: 0.8763 (m) cc_final: 0.8500 (m) REVERT: A 525 MET cc_start: 0.4430 (tpt) cc_final: 0.4140 (tpt) REVERT: A 559 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7174 (mm110) REVERT: A 568 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: A 602 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (m-40) REVERT: A 637 LYS cc_start: 0.7527 (mmmt) cc_final: 0.7286 (mmmm) REVERT: A 657 MET cc_start: 0.6174 (mmm) cc_final: 0.5941 (mmp) REVERT: A 669 GLN cc_start: 0.7571 (mt0) cc_final: 0.7091 (mt0) REVERT: A 673 MET cc_start: 0.6687 (mtt) cc_final: 0.6323 (mtm) REVERT: A 695 GLU cc_start: 0.7472 (mp0) cc_final: 0.7049 (mp0) REVERT: A 722 GLN cc_start: 0.6985 (mt0) cc_final: 0.6722 (mt0) REVERT: A 729 GLN cc_start: 0.7070 (tt0) cc_final: 0.6736 (tt0) REVERT: A 740 MET cc_start: 0.6638 (mmm) cc_final: 0.6106 (mtp) REVERT: A 752 ARG cc_start: 0.7033 (ttp80) cc_final: 0.6815 (ptt90) REVERT: A 759 TYR cc_start: 0.7983 (t80) cc_final: 0.7648 (t80) REVERT: A 816 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6910 (ttp-110) REVERT: A 840 ASP cc_start: 0.7718 (m-30) cc_final: 0.7345 (m-30) REVERT: A 843 LYS cc_start: 0.7132 (mttt) cc_final: 0.6901 (mtpm) REVERT: A 904 PHE cc_start: 0.7231 (m-80) cc_final: 0.7005 (m-10) REVERT: A 955 ILE cc_start: 0.8424 (mm) cc_final: 0.8047 (tp) REVERT: A 980 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6863 (ttmm) REVERT: A 983 LEU cc_start: 0.7912 (tp) cc_final: 0.7668 (tm) REVERT: B 8 ARG cc_start: 0.6861 (mpt180) cc_final: 0.6581 (mtt90) REVERT: B 17 LEU cc_start: 0.7814 (mt) cc_final: 0.7427 (mt) REVERT: B 20 MET cc_start: 0.7637 (mtp) cc_final: 0.7328 (mtm) REVERT: B 66 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 67 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: B 76 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6050 (mtm-85) REVERT: B 151 ASP cc_start: 0.5899 (p0) cc_final: 0.5620 (p0) REVERT: B 184 MET cc_start: 0.8793 (mmt) cc_final: 0.7523 (tpp) REVERT: B 263 LYS cc_start: 0.7852 (ptpt) cc_final: 0.7399 (pttt) REVERT: B 284 LYS cc_start: 0.7670 (mtmt) cc_final: 0.6933 (tmmt) REVERT: B 395 MET cc_start: 0.7264 (mmm) cc_final: 0.7027 (mmm) REVERT: B 398 MET cc_start: 0.7045 (tpt) cc_final: 0.6534 (mmt) REVERT: B 420 MET cc_start: 0.7923 (ttp) cc_final: 0.7514 (ttt) REVERT: B 481 SER cc_start: 0.7571 (t) cc_final: 0.7175 (p) REVERT: B 571 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: B 575 MET cc_start: 0.7438 (ttp) cc_final: 0.6418 (tpp) REVERT: B 594 ASP cc_start: 0.6907 (m-30) cc_final: 0.6436 (m-30) REVERT: B 653 MET cc_start: 0.7083 (tpp) cc_final: 0.6796 (tpp) REVERT: B 657 MET cc_start: 0.6992 (tmm) cc_final: 0.6775 (ttp) REVERT: B 730 ILE cc_start: 0.8149 (mt) cc_final: 0.7847 (mm) REVERT: B 733 ASP cc_start: 0.7064 (t0) cc_final: 0.6550 (t0) REVERT: B 736 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5773 (mm110) REVERT: B 740 MET cc_start: 0.7072 (mtp) cc_final: 0.6642 (mtt) REVERT: B 863 GLU cc_start: 0.7143 (tt0) cc_final: 0.6915 (mt-10) REVERT: B 891 LEU cc_start: 0.7026 (mt) cc_final: 0.6719 (mm) REVERT: B 892 CYS cc_start: 0.8108 (m) cc_final: 0.7300 (m) REVERT: B 987 ILE cc_start: 0.7757 (mm) cc_final: 0.7546 (mp) REVERT: C 8 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7137 (mtm-85) REVERT: C 17 LEU cc_start: 0.8079 (mp) cc_final: 0.7870 (mp) REVERT: C 20 MET cc_start: 0.6559 (mtp) cc_final: 0.6043 (mtm) REVERT: C 38 ILE cc_start: 0.8410 (mm) cc_final: 0.8006 (pp) REVERT: C 99 ASP cc_start: 0.7514 (t70) cc_final: 0.7298 (t0) REVERT: C 117 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8129 (mm) REVERT: C 120 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6686 (tm-30) REVERT: C 140 ILE cc_start: 0.8173 (mt) cc_final: 0.7875 (mp) REVERT: C 202 ASP cc_start: 0.8177 (m-30) cc_final: 0.7831 (m-30) REVERT: C 314 ARG cc_start: 0.5576 (ttm170) cc_final: 0.5301 (mtm110) REVERT: C 395 MET cc_start: 0.7530 (mmp) cc_final: 0.7315 (mmm) REVERT: C 405 LEU cc_start: 0.7460 (mp) cc_final: 0.7232 (mm) REVERT: C 417 GLU cc_start: 0.7581 (tp30) cc_final: 0.7288 (tp30) REVERT: C 422 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6140 (mt-10) REVERT: C 462 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7292 (t) REVERT: C 468 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7144 (ttm-80) REVERT: C 499 GLN cc_start: 0.7160 (tt0) cc_final: 0.6834 (tm-30) REVERT: C 530 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6431 (mm-40) REVERT: C 536 MET cc_start: 0.7150 (mmm) cc_final: 0.6925 (mtt) REVERT: C 575 MET cc_start: 0.6610 (ttm) cc_final: 0.6154 (ttm) REVERT: C 591 LYS cc_start: 0.5140 (mttt) cc_final: 0.4870 (mttt) REVERT: C 594 ASP cc_start: 0.4517 (t70) cc_final: 0.4228 (t70) REVERT: C 603 GLU cc_start: 0.5487 (mm-30) cc_final: 0.5258 (mm-30) REVERT: C 666 MET cc_start: 0.5763 (ttm) cc_final: 0.4864 (tpp) REVERT: C 668 LEU cc_start: 0.6329 (mt) cc_final: 0.5958 (mp) REVERT: C 705 LEU cc_start: 0.7901 (mt) cc_final: 0.7630 (mt) REVERT: C 707 LEU cc_start: 0.8067 (mt) cc_final: 0.7618 (mp) REVERT: C 729 GLN cc_start: 0.7114 (tt0) cc_final: 0.6492 (tp-100) REVERT: C 768 ARG cc_start: 0.6627 (mmt180) cc_final: 0.5796 (mtp180) REVERT: C 800 VAL cc_start: 0.7718 (t) cc_final: 0.7259 (m) REVERT: C 842 MET cc_start: 0.7193 (mtt) cc_final: 0.6910 (mtp) REVERT: C 857 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6831 (mp) REVERT: C 861 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6477 (p0) REVERT: C 873 GLU cc_start: 0.5484 (mt-10) cc_final: 0.5023 (mt-10) REVERT: C 887 LEU cc_start: 0.7297 (tp) cc_final: 0.6883 (tm) REVERT: C 904 PHE cc_start: 0.7720 (m-80) cc_final: 0.7239 (m-80) REVERT: C 932 ASN cc_start: 0.7702 (m-40) cc_final: 0.7462 (m-40) REVERT: C 940 GLN cc_start: 0.7345 (mt0) cc_final: 0.6953 (mt0) REVERT: C 943 ILE cc_start: 0.8062 (mt) cc_final: 0.7739 (mm) REVERT: C 963 GLU cc_start: 0.6542 (tt0) cc_final: 0.5935 (mm-30) REVERT: C 1023 LEU cc_start: 0.7957 (mt) cc_final: 0.7728 (mm) outliers start: 115 outliers final: 67 residues processed: 616 average time/residue: 1.1102 time to fit residues: 820.4685 Evaluate side-chains 626 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 543 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 0.0370 chunk 99 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 274 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24442 Z= 0.285 Angle : 0.650 23.570 33247 Z= 0.314 Chirality : 0.054 2.010 3913 Planarity : 0.005 0.052 4261 Dihedral : 6.079 103.913 3354 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.37 % Allowed : 17.77 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3134 helix: 2.00 (0.12), residues: 1699 sheet: 0.37 (0.24), residues: 447 loop : -0.14 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 187 HIS 0.009 0.001 HIS A 342 PHE 0.024 0.001 PHE C 599 TYR 0.019 0.002 TYR A 327 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 557 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: A 69 MET cc_start: 0.8530 (mmt) cc_final: 0.7924 (mmt) REVERT: A 99 ASP cc_start: 0.7840 (t70) cc_final: 0.7413 (t0) REVERT: A 117 LEU cc_start: 0.8273 (mt) cc_final: 0.8020 (mm) REVERT: A 128 THR cc_start: 0.8221 (m) cc_final: 0.7998 (p) REVERT: A 138 GLN cc_start: 0.7826 (mt0) cc_final: 0.7599 (mt0) REVERT: A 153 ASP cc_start: 0.7265 (m-30) cc_final: 0.7058 (m-30) REVERT: A 208 GLN cc_start: 0.7678 (mm110) cc_final: 0.7019 (mm110) REVERT: A 252 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6995 (ttmt) REVERT: A 261 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6880 (mtt-85) REVERT: A 269 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: A 278 ASP cc_start: 0.7434 (t0) cc_final: 0.7226 (t0) REVERT: A 292 LYS cc_start: 0.6963 (mttt) cc_final: 0.6591 (mtpp) REVERT: A 307 GLU cc_start: 0.7064 (tp30) cc_final: 0.6684 (tp30) REVERT: A 342 HIS cc_start: 0.7354 (t70) cc_final: 0.7001 (t-170) REVERT: A 438 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6450 (mp) REVERT: A 525 MET cc_start: 0.4268 (tpt) cc_final: 0.3984 (tpt) REVERT: A 559 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7181 (mm110) REVERT: A 568 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: A 580 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 602 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7185 (m-40) REVERT: A 657 MET cc_start: 0.6205 (mmm) cc_final: 0.5938 (mmp) REVERT: A 669 GLN cc_start: 0.7500 (mt0) cc_final: 0.7055 (mt0) REVERT: A 673 MET cc_start: 0.6732 (mtt) cc_final: 0.6353 (mtm) REVERT: A 690 SER cc_start: 0.8047 (m) cc_final: 0.7724 (p) REVERT: A 695 GLU cc_start: 0.7449 (mp0) cc_final: 0.7020 (mp0) REVERT: A 718 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7976 (ptt-90) REVERT: A 722 GLN cc_start: 0.6945 (mt0) cc_final: 0.6692 (mt0) REVERT: A 729 GLN cc_start: 0.7132 (tt0) cc_final: 0.6771 (tt0) REVERT: A 740 MET cc_start: 0.6616 (mmm) cc_final: 0.6239 (mtp) REVERT: A 752 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6823 (ptt90) REVERT: A 816 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7180 (ttp-110) REVERT: A 840 ASP cc_start: 0.7671 (m-30) cc_final: 0.7309 (m-30) REVERT: A 843 LYS cc_start: 0.7134 (mttt) cc_final: 0.6891 (mtpm) REVERT: A 904 PHE cc_start: 0.7246 (m-80) cc_final: 0.6997 (m-10) REVERT: A 955 ILE cc_start: 0.8480 (mm) cc_final: 0.7997 (tp) REVERT: A 959 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: A 980 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6863 (ttmm) REVERT: A 983 LEU cc_start: 0.7964 (tp) cc_final: 0.7692 (tm) REVERT: B 8 ARG cc_start: 0.6764 (mpt180) cc_final: 0.6563 (mtt90) REVERT: B 17 LEU cc_start: 0.7816 (mt) cc_final: 0.7592 (mt) REVERT: B 20 MET cc_start: 0.7686 (mtp) cc_final: 0.7396 (mtm) REVERT: B 66 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7549 (mt-10) REVERT: B 67 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: B 76 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6055 (mtm-85) REVERT: B 151 ASP cc_start: 0.5947 (p0) cc_final: 0.5657 (p0) REVERT: B 184 MET cc_start: 0.8785 (mmt) cc_final: 0.7501 (tpp) REVERT: B 263 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7407 (pttt) REVERT: B 284 LYS cc_start: 0.7656 (mtmt) cc_final: 0.6892 (tmmt) REVERT: B 395 MET cc_start: 0.7253 (mmm) cc_final: 0.7015 (mmm) REVERT: B 398 MET cc_start: 0.7051 (tpt) cc_final: 0.6537 (mmt) REVERT: B 420 MET cc_start: 0.7798 (ttp) cc_final: 0.7430 (ttt) REVERT: B 481 SER cc_start: 0.7579 (t) cc_final: 0.7183 (p) REVERT: B 571 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: B 575 MET cc_start: 0.7420 (ttp) cc_final: 0.6411 (tpp) REVERT: B 594 ASP cc_start: 0.7128 (m-30) cc_final: 0.6875 (m-30) REVERT: B 653 MET cc_start: 0.6950 (tpp) cc_final: 0.6653 (tpp) REVERT: B 657 MET cc_start: 0.6876 (tmm) cc_final: 0.6609 (ttp) REVERT: B 730 ILE cc_start: 0.8146 (mt) cc_final: 0.7841 (mm) REVERT: B 733 ASP cc_start: 0.7145 (t0) cc_final: 0.6570 (t0) REVERT: B 736 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5879 (mt0) REVERT: B 740 MET cc_start: 0.7062 (mtp) cc_final: 0.6655 (mtt) REVERT: B 802 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 863 GLU cc_start: 0.7103 (tt0) cc_final: 0.6835 (mt-10) REVERT: B 891 LEU cc_start: 0.7037 (mt) cc_final: 0.6723 (mm) REVERT: B 892 CYS cc_start: 0.8107 (m) cc_final: 0.7310 (m) REVERT: B 987 ILE cc_start: 0.7749 (mm) cc_final: 0.7528 (OUTLIER) REVERT: C 8 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7062 (mtm-85) REVERT: C 17 LEU cc_start: 0.8106 (mp) cc_final: 0.7866 (mp) REVERT: C 20 MET cc_start: 0.6537 (mtp) cc_final: 0.6022 (mtm) REVERT: C 29 LYS cc_start: 0.7483 (mmmt) cc_final: 0.7089 (tppp) REVERT: C 38 ILE cc_start: 0.8353 (mm) cc_final: 0.7987 (pp) REVERT: C 69 MET cc_start: 0.8087 (mmt) cc_final: 0.5473 (mmp) REVERT: C 99 ASP cc_start: 0.7525 (t70) cc_final: 0.7298 (t0) REVERT: C 117 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8126 (mm) REVERT: C 120 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6689 (tm-30) REVERT: C 140 ILE cc_start: 0.8191 (mt) cc_final: 0.7891 (mp) REVERT: C 202 ASP cc_start: 0.8224 (m-30) cc_final: 0.7953 (m-30) REVERT: C 240 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7239 (mt) REVERT: C 395 MET cc_start: 0.7539 (mmp) cc_final: 0.7325 (mmm) REVERT: C 405 LEU cc_start: 0.7452 (mp) cc_final: 0.7232 (mm) REVERT: C 422 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6235 (mt-10) REVERT: C 423 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.5992 (p0) REVERT: C 462 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7247 (t) REVERT: C 468 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7121 (ttm-80) REVERT: C 499 GLN cc_start: 0.7195 (tt0) cc_final: 0.6888 (tm-30) REVERT: C 530 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6419 (mm-40) REVERT: C 575 MET cc_start: 0.6643 (ttm) cc_final: 0.6171 (ttm) REVERT: C 591 LYS cc_start: 0.5165 (mttt) cc_final: 0.4938 (mttt) REVERT: C 608 GLU cc_start: 0.6646 (tt0) cc_final: 0.5986 (tp30) REVERT: C 666 MET cc_start: 0.5692 (ttm) cc_final: 0.4824 (tpp) REVERT: C 668 LEU cc_start: 0.6371 (mt) cc_final: 0.5972 (mp) REVERT: C 705 LEU cc_start: 0.7887 (mt) cc_final: 0.7609 (mt) REVERT: C 707 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7630 (mp) REVERT: C 729 GLN cc_start: 0.7082 (tt0) cc_final: 0.6461 (tp-100) REVERT: C 768 ARG cc_start: 0.6571 (mmt180) cc_final: 0.5901 (mmm160) REVERT: C 796 LYS cc_start: 0.7756 (tttm) cc_final: 0.7280 (ttmm) REVERT: C 800 VAL cc_start: 0.7728 (t) cc_final: 0.7250 (m) REVERT: C 842 MET cc_start: 0.7270 (mtt) cc_final: 0.6963 (mtp) REVERT: C 857 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6779 (mt) REVERT: C 861 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6443 (p0) REVERT: C 887 LEU cc_start: 0.7373 (tp) cc_final: 0.6965 (tm) REVERT: C 904 PHE cc_start: 0.7727 (m-80) cc_final: 0.7251 (m-80) REVERT: C 932 ASN cc_start: 0.7707 (m-40) cc_final: 0.7455 (m-40) REVERT: C 940 GLN cc_start: 0.7327 (mt0) cc_final: 0.6928 (mt0) REVERT: C 943 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 963 GLU cc_start: 0.6540 (tt0) cc_final: 0.5960 (mm-30) REVERT: C 1023 LEU cc_start: 0.7964 (mt) cc_final: 0.7717 (mm) outliers start: 139 outliers final: 83 residues processed: 634 average time/residue: 1.1088 time to fit residues: 838.4273 Evaluate side-chains 648 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 542 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 170 optimal weight: 30.0000 chunk 254 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 183 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 138 GLN C 148 ASN C 274 ASN C 531 ASN C 598 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24442 Z= 0.270 Angle : 0.644 23.377 33247 Z= 0.310 Chirality : 0.053 2.024 3913 Planarity : 0.005 0.051 4261 Dihedral : 6.034 103.615 3354 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.98 % Allowed : 18.39 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.15), residues: 3134 helix: 2.04 (0.12), residues: 1693 sheet: 0.39 (0.24), residues: 435 loop : -0.13 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 755 HIS 0.008 0.001 HIS A 342 PHE 0.032 0.001 PHE B 358 TYR 0.018 0.002 TYR A 327 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 549 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: A 69 MET cc_start: 0.8517 (mmt) cc_final: 0.8021 (mmt) REVERT: A 99 ASP cc_start: 0.7855 (t70) cc_final: 0.7423 (t0) REVERT: A 117 LEU cc_start: 0.8320 (mt) cc_final: 0.8103 (mm) REVERT: A 128 THR cc_start: 0.8220 (m) cc_final: 0.8015 (p) REVERT: A 138 GLN cc_start: 0.7812 (mt0) cc_final: 0.7595 (mt0) REVERT: A 208 GLN cc_start: 0.7670 (mm110) cc_final: 0.7018 (mm110) REVERT: A 252 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6982 (ttmt) REVERT: A 261 ARG cc_start: 0.7388 (mtt180) cc_final: 0.6924 (mtt-85) REVERT: A 269 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7146 (pp20) REVERT: A 292 LYS cc_start: 0.6957 (mttt) cc_final: 0.6584 (mtpp) REVERT: A 304 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6553 (pp20) REVERT: A 307 GLU cc_start: 0.7030 (tp30) cc_final: 0.6654 (tp30) REVERT: A 308 GLN cc_start: 0.6936 (tp-100) cc_final: 0.6660 (tp40) REVERT: A 342 HIS cc_start: 0.7286 (t70) cc_final: 0.6873 (t-170) REVERT: A 438 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6603 (mp) REVERT: A 447 SER cc_start: 0.8755 (m) cc_final: 0.8466 (m) REVERT: A 525 MET cc_start: 0.4247 (tpt) cc_final: 0.3951 (tpt) REVERT: A 559 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7173 (mm110) REVERT: A 568 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: A 580 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7980 (mp) REVERT: A 602 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7139 (m-40) REVERT: A 657 MET cc_start: 0.6191 (mmm) cc_final: 0.5919 (mmp) REVERT: A 669 GLN cc_start: 0.7494 (mt0) cc_final: 0.7057 (mt0) REVERT: A 673 MET cc_start: 0.6798 (mtt) cc_final: 0.6462 (mtm) REVERT: A 690 SER cc_start: 0.7977 (m) cc_final: 0.7663 (p) REVERT: A 718 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7987 (ptt-90) REVERT: A 722 GLN cc_start: 0.6932 (mt0) cc_final: 0.6690 (mt0) REVERT: A 729 GLN cc_start: 0.7098 (tt0) cc_final: 0.6807 (tt0) REVERT: A 740 MET cc_start: 0.6639 (mmm) cc_final: 0.6249 (mtp) REVERT: A 752 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6837 (ptt90) REVERT: A 816 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7186 (ttp-110) REVERT: A 840 ASP cc_start: 0.7701 (m-30) cc_final: 0.7332 (m-30) REVERT: A 843 LYS cc_start: 0.7152 (mttt) cc_final: 0.6919 (mtpm) REVERT: A 904 PHE cc_start: 0.7260 (m-80) cc_final: 0.7029 (m-10) REVERT: A 955 ILE cc_start: 0.8482 (mm) cc_final: 0.7997 (tp) REVERT: A 959 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7090 (pp20) REVERT: A 980 LYS cc_start: 0.7117 (ttmt) cc_final: 0.6834 (ttmm) REVERT: A 983 LEU cc_start: 0.7933 (tp) cc_final: 0.7669 (tm) REVERT: B 8 ARG cc_start: 0.6799 (mpt180) cc_final: 0.6545 (mtt90) REVERT: B 17 LEU cc_start: 0.7844 (mt) cc_final: 0.7583 (mt) REVERT: B 20 MET cc_start: 0.7686 (mtp) cc_final: 0.7361 (mtm) REVERT: B 66 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7584 (mt-10) REVERT: B 67 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: B 76 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6045 (mtm-85) REVERT: B 113 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8000 (p) REVERT: B 151 ASP cc_start: 0.5941 (p0) cc_final: 0.5661 (p0) REVERT: B 184 MET cc_start: 0.8780 (mmt) cc_final: 0.7480 (tpp) REVERT: B 263 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7338 (pttt) REVERT: B 284 LYS cc_start: 0.7637 (mtmt) cc_final: 0.6883 (tmmt) REVERT: B 395 MET cc_start: 0.7289 (mmm) cc_final: 0.7053 (mmm) REVERT: B 398 MET cc_start: 0.7010 (tpt) cc_final: 0.6607 (mmt) REVERT: B 420 MET cc_start: 0.7815 (ttp) cc_final: 0.7531 (ttt) REVERT: B 481 SER cc_start: 0.7586 (t) cc_final: 0.7271 (p) REVERT: B 571 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: B 575 MET cc_start: 0.7418 (ttp) cc_final: 0.6426 (tpp) REVERT: B 594 ASP cc_start: 0.7137 (m-30) cc_final: 0.6885 (m-30) REVERT: B 653 MET cc_start: 0.6891 (tpp) cc_final: 0.6590 (tpp) REVERT: B 657 MET cc_start: 0.6851 (tmm) cc_final: 0.6626 (ttp) REVERT: B 730 ILE cc_start: 0.8139 (mt) cc_final: 0.7832 (mm) REVERT: B 733 ASP cc_start: 0.7149 (t0) cc_final: 0.6568 (t0) REVERT: B 736 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.5975 (mt0) REVERT: B 740 MET cc_start: 0.7026 (mtp) cc_final: 0.6635 (mtt) REVERT: B 783 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.6635 (mpm) REVERT: B 802 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7763 (t80) REVERT: B 863 GLU cc_start: 0.7117 (tt0) cc_final: 0.6892 (mt-10) REVERT: B 891 LEU cc_start: 0.7054 (mt) cc_final: 0.6730 (mm) REVERT: B 892 CYS cc_start: 0.8106 (m) cc_final: 0.7314 (m) REVERT: B 987 ILE cc_start: 0.7528 (mm) cc_final: 0.7313 (mp) REVERT: B 1016 PHE cc_start: 0.7413 (m-80) cc_final: 0.7200 (m-10) REVERT: C 1 MET cc_start: 0.5940 (tpp) cc_final: 0.5632 (tpp) REVERT: C 8 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: C 17 LEU cc_start: 0.8110 (mp) cc_final: 0.7859 (mp) REVERT: C 20 MET cc_start: 0.6535 (mtp) cc_final: 0.6015 (mtm) REVERT: C 29 LYS cc_start: 0.7341 (mmmt) cc_final: 0.6951 (tppp) REVERT: C 38 ILE cc_start: 0.8350 (mm) cc_final: 0.7983 (pp) REVERT: C 99 ASP cc_start: 0.7528 (t70) cc_final: 0.7313 (t0) REVERT: C 117 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8135 (mm) REVERT: C 120 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6690 (tm-30) REVERT: C 137 LEU cc_start: 0.8051 (tp) cc_final: 0.7839 (tt) REVERT: C 140 ILE cc_start: 0.8197 (mt) cc_final: 0.7896 (mp) REVERT: C 202 ASP cc_start: 0.8220 (m-30) cc_final: 0.7954 (m-30) REVERT: C 240 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7301 (mt) REVERT: C 248 ASN cc_start: 0.6867 (t0) cc_final: 0.6476 (m-40) REVERT: C 314 ARG cc_start: 0.5613 (mtm180) cc_final: 0.5346 (mtm110) REVERT: C 395 MET cc_start: 0.7459 (mmp) cc_final: 0.7206 (mmm) REVERT: C 405 LEU cc_start: 0.7475 (mp) cc_final: 0.7247 (mm) REVERT: C 422 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6241 (mt-10) REVERT: C 423 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.6048 (p0) REVERT: C 462 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7277 (t) REVERT: C 468 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7274 (ttp-110) REVERT: C 499 GLN cc_start: 0.7201 (tt0) cc_final: 0.6983 (tm-30) REVERT: C 530 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6439 (mm-40) REVERT: C 536 MET cc_start: 0.6808 (mtt) cc_final: 0.6465 (ttm) REVERT: C 575 MET cc_start: 0.6630 (ttm) cc_final: 0.6178 (ttm) REVERT: C 591 LYS cc_start: 0.5186 (mttt) cc_final: 0.4917 (mttt) REVERT: C 594 ASP cc_start: 0.4543 (t70) cc_final: 0.4263 (t70) REVERT: C 608 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: C 666 MET cc_start: 0.5719 (ttm) cc_final: 0.4850 (tpp) REVERT: C 668 LEU cc_start: 0.6382 (mt) cc_final: 0.5961 (mp) REVERT: C 705 LEU cc_start: 0.7912 (mt) cc_final: 0.7641 (mt) REVERT: C 707 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7590 (mp) REVERT: C 729 GLN cc_start: 0.7084 (tt0) cc_final: 0.6466 (tp-100) REVERT: C 768 ARG cc_start: 0.6543 (mmt180) cc_final: 0.5816 (mmm160) REVERT: C 796 LYS cc_start: 0.7768 (tttm) cc_final: 0.7298 (ttmm) REVERT: C 800 VAL cc_start: 0.7674 (t) cc_final: 0.7203 (m) REVERT: C 818 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: C 842 MET cc_start: 0.7251 (mtt) cc_final: 0.6955 (mtp) REVERT: C 861 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6420 (p0) REVERT: C 887 LEU cc_start: 0.7333 (tp) cc_final: 0.6930 (tm) REVERT: C 904 PHE cc_start: 0.7703 (m-80) cc_final: 0.7238 (m-80) REVERT: C 932 ASN cc_start: 0.7698 (m-40) cc_final: 0.7470 (m-40) REVERT: C 940 GLN cc_start: 0.7324 (mt0) cc_final: 0.6918 (mt0) REVERT: C 943 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7785 (mm) REVERT: C 963 GLU cc_start: 0.6542 (tt0) cc_final: 0.5953 (mm-30) REVERT: C 1023 LEU cc_start: 0.7967 (mt) cc_final: 0.7727 (mm) outliers start: 129 outliers final: 76 residues processed: 623 average time/residue: 1.0744 time to fit residues: 795.1085 Evaluate side-chains 637 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 534 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 204 optimal weight: 0.0170 chunk 148 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN B 827 ASN C 148 ASN C 274 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24442 Z= 0.267 Angle : 0.646 23.366 33247 Z= 0.310 Chirality : 0.053 2.027 3913 Planarity : 0.005 0.051 4261 Dihedral : 6.017 103.460 3354 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.95 % Allowed : 19.13 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3134 helix: 2.04 (0.12), residues: 1691 sheet: 0.42 (0.24), residues: 431 loop : -0.20 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 755 HIS 0.008 0.001 HIS A 342 PHE 0.029 0.001 PHE B 358 TYR 0.018 0.002 TYR A 327 ARG 0.003 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 550 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: A 69 MET cc_start: 0.8482 (mmt) cc_final: 0.7949 (mmt) REVERT: A 99 ASP cc_start: 0.7834 (t70) cc_final: 0.7438 (t0) REVERT: A 117 LEU cc_start: 0.8318 (mt) cc_final: 0.8101 (mm) REVERT: A 128 THR cc_start: 0.8219 (m) cc_final: 0.8015 (p) REVERT: A 138 GLN cc_start: 0.7809 (mt0) cc_final: 0.7589 (mt0) REVERT: A 208 GLN cc_start: 0.7654 (mm110) cc_final: 0.7004 (mm110) REVERT: A 252 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6991 (ttmt) REVERT: A 269 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7145 (pp20) REVERT: A 292 LYS cc_start: 0.6959 (mttt) cc_final: 0.6587 (mtpp) REVERT: A 307 GLU cc_start: 0.7032 (tp30) cc_final: 0.6656 (tp30) REVERT: A 308 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6662 (tp40) REVERT: A 342 HIS cc_start: 0.7273 (t70) cc_final: 0.6863 (t-170) REVERT: A 438 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6563 (mp) REVERT: A 447 SER cc_start: 0.8755 (m) cc_final: 0.8464 (m) REVERT: A 525 MET cc_start: 0.4243 (tpt) cc_final: 0.3951 (tpt) REVERT: A 554 LEU cc_start: 0.8086 (tt) cc_final: 0.7883 (tp) REVERT: A 559 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7187 (mm110) REVERT: A 568 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 580 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 602 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7132 (m-40) REVERT: A 657 MET cc_start: 0.6177 (mmm) cc_final: 0.5930 (mmp) REVERT: A 673 MET cc_start: 0.6748 (mtt) cc_final: 0.6381 (mtm) REVERT: A 690 SER cc_start: 0.7982 (m) cc_final: 0.7675 (p) REVERT: A 718 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7983 (ptt-90) REVERT: A 729 GLN cc_start: 0.7113 (tt0) cc_final: 0.6814 (tt0) REVERT: A 740 MET cc_start: 0.6706 (mmm) cc_final: 0.6294 (mtp) REVERT: A 752 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6748 (ptt90) REVERT: A 816 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7192 (ttp-110) REVERT: A 840 ASP cc_start: 0.7668 (m-30) cc_final: 0.7305 (m-30) REVERT: A 843 LYS cc_start: 0.7114 (mttt) cc_final: 0.6872 (mtpm) REVERT: A 904 PHE cc_start: 0.7271 (m-80) cc_final: 0.7037 (m-10) REVERT: A 955 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 959 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7103 (pp20) REVERT: A 980 LYS cc_start: 0.7093 (ttmt) cc_final: 0.6823 (ttmm) REVERT: A 983 LEU cc_start: 0.7924 (tp) cc_final: 0.7663 (tm) REVERT: B 8 ARG cc_start: 0.6782 (mpt180) cc_final: 0.6548 (mtt90) REVERT: B 17 LEU cc_start: 0.7891 (mt) cc_final: 0.7624 (mt) REVERT: B 20 MET cc_start: 0.7673 (mtp) cc_final: 0.7350 (mtm) REVERT: B 66 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 67 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: B 76 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6049 (mtm-85) REVERT: B 113 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.8002 (p) REVERT: B 151 ASP cc_start: 0.5942 (p0) cc_final: 0.5664 (p0) REVERT: B 184 MET cc_start: 0.8780 (mmt) cc_final: 0.7471 (tpp) REVERT: B 263 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7365 (pttt) REVERT: B 395 MET cc_start: 0.7301 (mmm) cc_final: 0.7065 (mmm) REVERT: B 398 MET cc_start: 0.7021 (tpt) cc_final: 0.6624 (mmt) REVERT: B 420 MET cc_start: 0.7784 (ttp) cc_final: 0.7536 (ttt) REVERT: B 481 SER cc_start: 0.7616 (t) cc_final: 0.7266 (p) REVERT: B 571 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: B 575 MET cc_start: 0.7426 (ttp) cc_final: 0.6436 (tpp) REVERT: B 594 ASP cc_start: 0.7125 (m-30) cc_final: 0.6857 (m-30) REVERT: B 653 MET cc_start: 0.6840 (tpp) cc_final: 0.6555 (tpp) REVERT: B 657 MET cc_start: 0.6787 (tmm) cc_final: 0.6544 (ttp) REVERT: B 730 ILE cc_start: 0.8129 (mt) cc_final: 0.7827 (mm) REVERT: B 733 ASP cc_start: 0.7152 (t0) cc_final: 0.6581 (t0) REVERT: B 736 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: B 740 MET cc_start: 0.7026 (mtp) cc_final: 0.6634 (mtt) REVERT: B 783 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.6650 (mpm) REVERT: B 802 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 852 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6815 (tp) REVERT: B 891 LEU cc_start: 0.7059 (mt) cc_final: 0.6735 (mm) REVERT: B 892 CYS cc_start: 0.8104 (m) cc_final: 0.7315 (m) REVERT: B 987 ILE cc_start: 0.7555 (mm) cc_final: 0.7319 (mp) REVERT: B 1016 PHE cc_start: 0.7442 (m-80) cc_final: 0.7185 (m-10) REVERT: C 1 MET cc_start: 0.5666 (tpp) cc_final: 0.5324 (tpp) REVERT: C 8 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7104 (mtm-85) REVERT: C 17 LEU cc_start: 0.8113 (mp) cc_final: 0.7855 (mp) REVERT: C 20 MET cc_start: 0.6550 (mtp) cc_final: 0.5974 (mtm) REVERT: C 29 LYS cc_start: 0.7327 (mmmt) cc_final: 0.6936 (tppp) REVERT: C 38 ILE cc_start: 0.8343 (mm) cc_final: 0.7985 (pp) REVERT: C 117 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 120 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6691 (tm-30) REVERT: C 137 LEU cc_start: 0.8132 (tp) cc_final: 0.7921 (tt) REVERT: C 140 ILE cc_start: 0.8212 (mt) cc_final: 0.7907 (mp) REVERT: C 202 ASP cc_start: 0.8223 (m-30) cc_final: 0.7963 (m-30) REVERT: C 240 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7273 (mt) REVERT: C 248 ASN cc_start: 0.6871 (t0) cc_final: 0.6430 (m-40) REVERT: C 292 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6769 (mttt) REVERT: C 314 ARG cc_start: 0.5586 (ttm170) cc_final: 0.5330 (ttm110) REVERT: C 363 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.7532 (mmt-90) REVERT: C 395 MET cc_start: 0.7431 (mmp) cc_final: 0.7181 (mmm) REVERT: C 405 LEU cc_start: 0.7478 (mp) cc_final: 0.7254 (mm) REVERT: C 422 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6193 (mt-10) REVERT: C 423 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6065 (p0) REVERT: C 462 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7299 (t) REVERT: C 468 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7271 (ttp-110) REVERT: C 499 GLN cc_start: 0.7213 (tt0) cc_final: 0.6877 (tm-30) REVERT: C 530 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6698 (mt0) REVERT: C 536 MET cc_start: 0.6790 (mtt) cc_final: 0.6443 (ttm) REVERT: C 575 MET cc_start: 0.6615 (ttm) cc_final: 0.6160 (ttm) REVERT: C 591 LYS cc_start: 0.5148 (mttt) cc_final: 0.4871 (mttt) REVERT: C 594 ASP cc_start: 0.4546 (t70) cc_final: 0.4256 (t70) REVERT: C 608 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5986 (tp30) REVERT: C 657 MET cc_start: 0.7604 (ttm) cc_final: 0.7320 (ttp) REVERT: C 666 MET cc_start: 0.5739 (ttm) cc_final: 0.4851 (tpp) REVERT: C 668 LEU cc_start: 0.6340 (mt) cc_final: 0.5924 (mp) REVERT: C 683 ASN cc_start: 0.7487 (t0) cc_final: 0.6977 (t0) REVERT: C 705 LEU cc_start: 0.7932 (mt) cc_final: 0.7636 (mt) REVERT: C 707 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 729 GLN cc_start: 0.7058 (tt0) cc_final: 0.6456 (tp-100) REVERT: C 768 ARG cc_start: 0.6587 (mmt180) cc_final: 0.5832 (mmm160) REVERT: C 796 LYS cc_start: 0.7736 (tttm) cc_final: 0.7261 (ttmm) REVERT: C 800 VAL cc_start: 0.7710 (t) cc_final: 0.7236 (m) REVERT: C 818 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: C 842 MET cc_start: 0.7263 (mtt) cc_final: 0.6971 (mtp) REVERT: C 861 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6526 (p0) REVERT: C 887 LEU cc_start: 0.7439 (tp) cc_final: 0.7025 (tm) REVERT: C 904 PHE cc_start: 0.7691 (m-80) cc_final: 0.7159 (m-80) REVERT: C 932 ASN cc_start: 0.7704 (m-40) cc_final: 0.7440 (m-40) REVERT: C 940 GLN cc_start: 0.7278 (mt0) cc_final: 0.6879 (mt0) REVERT: C 943 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7789 (mm) REVERT: C 963 GLU cc_start: 0.6486 (tt0) cc_final: 0.5797 (mm-30) REVERT: C 1023 LEU cc_start: 0.7969 (mt) cc_final: 0.7726 (mm) outliers start: 128 outliers final: 74 residues processed: 621 average time/residue: 1.1170 time to fit residues: 827.7672 Evaluate side-chains 645 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 541 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 783 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1004 THR Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 0.0470 chunk 253 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN A 722 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 274 ASN C 531 ASN C 598 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24442 Z= 0.217 Angle : 0.624 23.529 33247 Z= 0.296 Chirality : 0.053 2.030 3913 Planarity : 0.004 0.051 4261 Dihedral : 5.912 103.557 3354 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.15), residues: 3134 helix: 2.14 (0.12), residues: 1692 sheet: 0.43 (0.24), residues: 432 loop : -0.17 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 755 HIS 0.008 0.001 HIS A 342 PHE 0.024 0.001 PHE A 380 TYR 0.016 0.001 TYR A 664 ARG 0.003 0.000 ARG C 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 543 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: A 69 MET cc_start: 0.8458 (mmt) cc_final: 0.7863 (mmt) REVERT: A 81 ASN cc_start: 0.7045 (m-40) cc_final: 0.6682 (m-40) REVERT: A 99 ASP cc_start: 0.7840 (t70) cc_final: 0.7411 (t0) REVERT: A 117 LEU cc_start: 0.8334 (mt) cc_final: 0.8072 (mm) REVERT: A 138 GLN cc_start: 0.7794 (mt0) cc_final: 0.7583 (mt0) REVERT: A 208 GLN cc_start: 0.7623 (mm110) cc_final: 0.6988 (mm110) REVERT: A 252 LYS cc_start: 0.7181 (ttpt) cc_final: 0.6976 (ttmt) REVERT: A 269 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: A 292 LYS cc_start: 0.6944 (mttt) cc_final: 0.6563 (mtpp) REVERT: A 304 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6537 (pp20) REVERT: A 307 GLU cc_start: 0.7018 (tp30) cc_final: 0.6647 (tp30) REVERT: A 308 GLN cc_start: 0.6919 (tp-100) cc_final: 0.6613 (tp-100) REVERT: A 342 HIS cc_start: 0.7273 (t70) cc_final: 0.6869 (t-170) REVERT: A 438 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6559 (mp) REVERT: A 447 SER cc_start: 0.8759 (m) cc_final: 0.8502 (m) REVERT: A 525 MET cc_start: 0.4234 (tpt) cc_final: 0.3967 (tpt) REVERT: A 559 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7187 (mm110) REVERT: A 568 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: A 580 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 602 ASN cc_start: 0.7426 (t0) cc_final: 0.7132 (m-40) REVERT: A 657 MET cc_start: 0.6164 (mmm) cc_final: 0.5925 (mmp) REVERT: A 669 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: A 673 MET cc_start: 0.6739 (mtt) cc_final: 0.6386 (mtm) REVERT: A 690 SER cc_start: 0.8071 (m) cc_final: 0.7771 (p) REVERT: A 718 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7970 (ptt-90) REVERT: A 727 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5913 (mt0) REVERT: A 729 GLN cc_start: 0.7113 (tt0) cc_final: 0.6797 (tt0) REVERT: A 740 MET cc_start: 0.6624 (mmm) cc_final: 0.6244 (mtp) REVERT: A 752 ARG cc_start: 0.7007 (ttp80) cc_final: 0.6723 (ptt90) REVERT: A 816 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6883 (ttp-110) REVERT: A 840 ASP cc_start: 0.7712 (m-30) cc_final: 0.7341 (m-30) REVERT: A 843 LYS cc_start: 0.7135 (mttt) cc_final: 0.6892 (mtpm) REVERT: A 904 PHE cc_start: 0.7253 (m-80) cc_final: 0.7002 (m-10) REVERT: A 955 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 959 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: A 980 LYS cc_start: 0.7086 (ttmt) cc_final: 0.6831 (ttmm) REVERT: A 983 LEU cc_start: 0.7905 (tp) cc_final: 0.7661 (tm) REVERT: B 17 LEU cc_start: 0.7893 (mt) cc_final: 0.7488 (mt) REVERT: B 20 MET cc_start: 0.7670 (mtp) cc_final: 0.7352 (mtm) REVERT: B 66 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 67 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: B 76 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6032 (mtm-85) REVERT: B 113 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (p) REVERT: B 151 ASP cc_start: 0.5928 (p0) cc_final: 0.5641 (p0) REVERT: B 184 MET cc_start: 0.8753 (mmt) cc_final: 0.7447 (tpp) REVERT: B 263 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7324 (pttt) REVERT: B 284 LYS cc_start: 0.7551 (mmmm) cc_final: 0.6058 (tmmt) REVERT: B 395 MET cc_start: 0.7287 (mmm) cc_final: 0.7044 (mmm) REVERT: B 420 MET cc_start: 0.7775 (ttp) cc_final: 0.7544 (ttt) REVERT: B 481 SER cc_start: 0.7611 (t) cc_final: 0.7283 (p) REVERT: B 571 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: B 575 MET cc_start: 0.7425 (ttp) cc_final: 0.6360 (tpp) REVERT: B 594 ASP cc_start: 0.7063 (m-30) cc_final: 0.6791 (m-30) REVERT: B 653 MET cc_start: 0.6758 (tpp) cc_final: 0.6469 (tpp) REVERT: B 657 MET cc_start: 0.6935 (tmm) cc_final: 0.6655 (ttp) REVERT: B 730 ILE cc_start: 0.8134 (mt) cc_final: 0.7825 (mm) REVERT: B 733 ASP cc_start: 0.7155 (t0) cc_final: 0.6607 (t0) REVERT: B 736 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.5654 (mm110) REVERT: B 740 MET cc_start: 0.7048 (mtp) cc_final: 0.6629 (mtt) REVERT: B 785 GLU cc_start: 0.6993 (tt0) cc_final: 0.6519 (mp0) REVERT: B 802 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 818 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 852 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6863 (tp) REVERT: B 863 GLU cc_start: 0.7103 (tt0) cc_final: 0.6891 (mt-10) REVERT: B 891 LEU cc_start: 0.7059 (mt) cc_final: 0.6750 (mm) REVERT: B 892 CYS cc_start: 0.8161 (m) cc_final: 0.7382 (m) REVERT: B 925 MET cc_start: 0.7932 (tmm) cc_final: 0.7246 (tmm) REVERT: B 987 ILE cc_start: 0.7570 (mm) cc_final: 0.7351 (mp) REVERT: B 1016 PHE cc_start: 0.7420 (m-80) cc_final: 0.7159 (m-10) REVERT: C 1 MET cc_start: 0.5635 (tpp) cc_final: 0.5309 (tpp) REVERT: C 8 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.7077 (mtm-85) REVERT: C 20 MET cc_start: 0.6585 (mtp) cc_final: 0.6026 (mtm) REVERT: C 29 LYS cc_start: 0.7345 (mmmt) cc_final: 0.6878 (tppp) REVERT: C 38 ILE cc_start: 0.8348 (mm) cc_final: 0.8004 (pp) REVERT: C 69 MET cc_start: 0.8111 (mmt) cc_final: 0.5332 (mmp) REVERT: C 117 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8128 (mm) REVERT: C 120 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6700 (tm-30) REVERT: C 137 LEU cc_start: 0.8131 (tp) cc_final: 0.7921 (tt) REVERT: C 140 ILE cc_start: 0.8216 (mt) cc_final: 0.7919 (mp) REVERT: C 164 GLU cc_start: 0.5716 (tt0) cc_final: 0.5436 (mt-10) REVERT: C 197 GLN cc_start: 0.8135 (mp10) cc_final: 0.7855 (mp10) REVERT: C 202 ASP cc_start: 0.8205 (m-30) cc_final: 0.7934 (m-30) REVERT: C 240 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7247 (mt) REVERT: C 248 ASN cc_start: 0.6865 (t0) cc_final: 0.6605 (m-40) REVERT: C 314 ARG cc_start: 0.5516 (ttm170) cc_final: 0.5247 (ttm110) REVERT: C 405 LEU cc_start: 0.7433 (mp) cc_final: 0.7210 (mm) REVERT: C 422 GLU cc_start: 0.6343 (mt-10) cc_final: 0.6105 (mt-10) REVERT: C 423 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.6027 (p0) REVERT: C 462 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7220 (t) REVERT: C 468 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7057 (ttm-80) REVERT: C 499 GLN cc_start: 0.7197 (tt0) cc_final: 0.6887 (tm-30) REVERT: C 530 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6474 (mm-40) REVERT: C 536 MET cc_start: 0.6789 (mtt) cc_final: 0.6467 (ttm) REVERT: C 575 MET cc_start: 0.6569 (ttm) cc_final: 0.6113 (ttm) REVERT: C 591 LYS cc_start: 0.5169 (mttt) cc_final: 0.4888 (mttt) REVERT: C 594 ASP cc_start: 0.4727 (t70) cc_final: 0.4424 (t70) REVERT: C 608 GLU cc_start: 0.6649 (tt0) cc_final: 0.5955 (tp30) REVERT: C 657 MET cc_start: 0.7581 (ttm) cc_final: 0.7320 (ttp) REVERT: C 666 MET cc_start: 0.5777 (ttm) cc_final: 0.4908 (tpp) REVERT: C 668 LEU cc_start: 0.6301 (mt) cc_final: 0.5906 (mp) REVERT: C 683 ASN cc_start: 0.7466 (t0) cc_final: 0.6953 (t0) REVERT: C 705 LEU cc_start: 0.7870 (mt) cc_final: 0.7593 (mt) REVERT: C 707 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7553 (mp) REVERT: C 729 GLN cc_start: 0.7067 (tt0) cc_final: 0.6461 (tp-100) REVERT: C 768 ARG cc_start: 0.6573 (mmt180) cc_final: 0.5847 (mmm160) REVERT: C 796 LYS cc_start: 0.7689 (tttm) cc_final: 0.7235 (ttmm) REVERT: C 799 MET cc_start: 0.7650 (mmp) cc_final: 0.7437 (mmt) REVERT: C 800 VAL cc_start: 0.7720 (t) cc_final: 0.7233 (m) REVERT: C 818 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: C 842 MET cc_start: 0.7213 (mtt) cc_final: 0.6909 (mtp) REVERT: C 861 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6505 (p0) REVERT: C 887 LEU cc_start: 0.7307 (tp) cc_final: 0.6920 (tm) REVERT: C 904 PHE cc_start: 0.7738 (m-80) cc_final: 0.7195 (m-80) REVERT: C 932 ASN cc_start: 0.7698 (m-40) cc_final: 0.7454 (m-40) REVERT: C 940 GLN cc_start: 0.7331 (mt0) cc_final: 0.6930 (mt0) REVERT: C 943 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7723 (mm) REVERT: C 1012 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7562 (m170) REVERT: C 1023 LEU cc_start: 0.7985 (mt) cc_final: 0.7751 (mm) outliers start: 109 outliers final: 64 residues processed: 611 average time/residue: 1.1153 time to fit residues: 807.1968 Evaluate side-chains 626 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 534 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 669 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 LYS Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1004 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.6980 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 191 optimal weight: 40.0000 chunk 151 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 274 ASN C 415 ASN C 531 ASN C 598 ASN C 795 ASN C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24442 Z= 0.292 Angle : 0.662 23.658 33247 Z= 0.318 Chirality : 0.054 2.011 3913 Planarity : 0.005 0.051 4261 Dihedral : 6.004 103.359 3354 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.06 % Allowed : 20.13 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3134 helix: 1.99 (0.12), residues: 1691 sheet: 0.39 (0.24), residues: 431 loop : -0.21 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 755 HIS 0.007 0.001 HIS A 342 PHE 0.026 0.002 PHE A 380 TYR 0.019 0.002 TYR A 327 ARG 0.006 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 544 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: A 69 MET cc_start: 0.8450 (mmt) cc_final: 0.8001 (mmt) REVERT: A 81 ASN cc_start: 0.7182 (m-40) cc_final: 0.6771 (m-40) REVERT: A 99 ASP cc_start: 0.7855 (t70) cc_final: 0.7421 (t0) REVERT: A 117 LEU cc_start: 0.8288 (mt) cc_final: 0.8065 (mm) REVERT: A 138 GLN cc_start: 0.7814 (mt0) cc_final: 0.7592 (mt0) REVERT: A 208 GLN cc_start: 0.7687 (mm110) cc_final: 0.7018 (mm110) REVERT: A 252 LYS cc_start: 0.7224 (ttpt) cc_final: 0.7000 (ttmt) REVERT: A 269 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: A 292 LYS cc_start: 0.6975 (mttt) cc_final: 0.6605 (mtpp) REVERT: A 307 GLU cc_start: 0.7043 (tp30) cc_final: 0.6669 (tp30) REVERT: A 308 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6658 (tp40) REVERT: A 316 ASN cc_start: 0.8139 (m-40) cc_final: 0.7934 (m-40) REVERT: A 342 HIS cc_start: 0.7293 (t70) cc_final: 0.6887 (t-170) REVERT: A 438 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6605 (mp) REVERT: A 447 SER cc_start: 0.8755 (m) cc_final: 0.8470 (m) REVERT: A 525 MET cc_start: 0.4250 (tpt) cc_final: 0.3984 (tpt) REVERT: A 559 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7196 (mm110) REVERT: A 568 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: A 580 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 602 ASN cc_start: 0.7369 (t0) cc_final: 0.7071 (m-40) REVERT: A 657 MET cc_start: 0.6204 (mmm) cc_final: 0.5921 (mmp) REVERT: A 669 GLN cc_start: 0.7538 (mt0) cc_final: 0.7052 (mt0) REVERT: A 673 MET cc_start: 0.6757 (mtt) cc_final: 0.6420 (mtm) REVERT: A 690 SER cc_start: 0.8085 (m) cc_final: 0.7791 (p) REVERT: A 718 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7987 (ptt-90) REVERT: A 727 GLN cc_start: 0.6220 (OUTLIER) cc_final: 0.5977 (mt0) REVERT: A 729 GLN cc_start: 0.7123 (tt0) cc_final: 0.6831 (tt0) REVERT: A 740 MET cc_start: 0.6702 (mmm) cc_final: 0.6310 (mtp) REVERT: A 752 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6818 (ptt90) REVERT: A 816 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6776 (ttp-110) REVERT: A 840 ASP cc_start: 0.7673 (m-30) cc_final: 0.7311 (m-30) REVERT: A 843 LYS cc_start: 0.7156 (mttt) cc_final: 0.6903 (mtpm) REVERT: A 904 PHE cc_start: 0.7205 (m-80) cc_final: 0.6965 (m-10) REVERT: A 955 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 959 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: A 980 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6838 (ttmm) REVERT: A 983 LEU cc_start: 0.7982 (tp) cc_final: 0.7726 (tm) REVERT: B 8 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6541 (mtt-85) REVERT: B 17 LEU cc_start: 0.7893 (mt) cc_final: 0.7478 (mt) REVERT: B 20 MET cc_start: 0.7653 (mtp) cc_final: 0.7347 (mtm) REVERT: B 66 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 67 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: B 69 MET cc_start: 0.8111 (mmt) cc_final: 0.7343 (mmp) REVERT: B 76 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5970 (mtm-85) REVERT: B 95 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: B 113 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 151 ASP cc_start: 0.5948 (p0) cc_final: 0.5662 (p0) REVERT: B 184 MET cc_start: 0.8779 (mmt) cc_final: 0.7468 (tpp) REVERT: B 263 LYS cc_start: 0.7797 (ptpt) cc_final: 0.7324 (pttt) REVERT: B 395 MET cc_start: 0.7267 (mmm) cc_final: 0.7033 (mmm) REVERT: B 420 MET cc_start: 0.7794 (ttp) cc_final: 0.7559 (ttt) REVERT: B 481 SER cc_start: 0.7618 (t) cc_final: 0.7292 (p) REVERT: B 571 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: B 575 MET cc_start: 0.7430 (ttp) cc_final: 0.6438 (tpp) REVERT: B 594 ASP cc_start: 0.7085 (m-30) cc_final: 0.6885 (m-30) REVERT: B 653 MET cc_start: 0.6765 (tpp) cc_final: 0.6465 (tpp) REVERT: B 657 MET cc_start: 0.6945 (tmm) cc_final: 0.6653 (ttp) REVERT: B 730 ILE cc_start: 0.8135 (mt) cc_final: 0.7837 (mm) REVERT: B 733 ASP cc_start: 0.7119 (t0) cc_final: 0.6537 (t0) REVERT: B 736 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.6033 (mt0) REVERT: B 740 MET cc_start: 0.6993 (mtp) cc_final: 0.6647 (mtt) REVERT: B 785 GLU cc_start: 0.7013 (tt0) cc_final: 0.6527 (mp0) REVERT: B 802 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 852 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6861 (tp) REVERT: B 863 GLU cc_start: 0.7135 (tt0) cc_final: 0.6880 (mt-10) REVERT: B 891 LEU cc_start: 0.7060 (mt) cc_final: 0.6739 (mm) REVERT: B 892 CYS cc_start: 0.8135 (m) cc_final: 0.7380 (m) REVERT: B 987 ILE cc_start: 0.7551 (mm) cc_final: 0.7345 (mp) REVERT: B 1016 PHE cc_start: 0.7442 (m-80) cc_final: 0.7178 (m-10) REVERT: C 1 MET cc_start: 0.5817 (tpp) cc_final: 0.5497 (tpp) REVERT: C 8 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7182 (mtm-85) REVERT: C 17 LEU cc_start: 0.8173 (mp) cc_final: 0.7898 (mp) REVERT: C 20 MET cc_start: 0.6582 (mtp) cc_final: 0.6043 (mtm) REVERT: C 29 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6965 (tppp) REVERT: C 38 ILE cc_start: 0.8343 (mm) cc_final: 0.7983 (pp) REVERT: C 69 MET cc_start: 0.8112 (mmt) cc_final: 0.5347 (mmp) REVERT: C 117 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 120 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6686 (tm-30) REVERT: C 137 LEU cc_start: 0.8130 (tp) cc_final: 0.7929 (tt) REVERT: C 140 ILE cc_start: 0.8222 (mt) cc_final: 0.7918 (mp) REVERT: C 164 GLU cc_start: 0.5720 (tt0) cc_final: 0.5437 (mt-10) REVERT: C 202 ASP cc_start: 0.8221 (m-30) cc_final: 0.7956 (m-30) REVERT: C 240 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7274 (mt) REVERT: C 248 ASN cc_start: 0.6846 (t0) cc_final: 0.6599 (m-40) REVERT: C 314 ARG cc_start: 0.5578 (ttm170) cc_final: 0.5305 (ttm110) REVERT: C 405 LEU cc_start: 0.7490 (mp) cc_final: 0.7272 (mm) REVERT: C 423 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.6046 (p0) REVERT: C 462 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7290 (t) REVERT: C 468 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7253 (ttp-110) REVERT: C 499 GLN cc_start: 0.7261 (tt0) cc_final: 0.6940 (tm-30) REVERT: C 530 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6699 (mt0) REVERT: C 536 MET cc_start: 0.6781 (mtt) cc_final: 0.6399 (ttm) REVERT: C 575 MET cc_start: 0.6605 (ttm) cc_final: 0.6156 (ttm) REVERT: C 591 LYS cc_start: 0.4866 (mttt) cc_final: 0.4611 (mttt) REVERT: C 594 ASP cc_start: 0.4728 (t70) cc_final: 0.4425 (t70) REVERT: C 608 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5955 (tp30) REVERT: C 657 MET cc_start: 0.7597 (ttm) cc_final: 0.7298 (ttp) REVERT: C 666 MET cc_start: 0.5806 (ttm) cc_final: 0.4936 (tpp) REVERT: C 668 LEU cc_start: 0.6347 (mt) cc_final: 0.5930 (mp) REVERT: C 683 ASN cc_start: 0.7555 (t0) cc_final: 0.7038 (t0) REVERT: C 705 LEU cc_start: 0.7908 (mt) cc_final: 0.7634 (mt) REVERT: C 707 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7563 (mp) REVERT: C 729 GLN cc_start: 0.7049 (tt0) cc_final: 0.6448 (tp-100) REVERT: C 768 ARG cc_start: 0.6585 (mmt180) cc_final: 0.5853 (mmm160) REVERT: C 796 LYS cc_start: 0.7687 (tttm) cc_final: 0.7215 (ttmm) REVERT: C 800 VAL cc_start: 0.7712 (t) cc_final: 0.7248 (m) REVERT: C 818 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: C 842 MET cc_start: 0.7265 (mtt) cc_final: 0.6962 (mtp) REVERT: C 861 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6547 (p0) REVERT: C 887 LEU cc_start: 0.7433 (tp) cc_final: 0.7033 (tm) REVERT: C 904 PHE cc_start: 0.7679 (m-80) cc_final: 0.7216 (m-80) REVERT: C 932 ASN cc_start: 0.7704 (m-40) cc_final: 0.7464 (m-40) REVERT: C 940 GLN cc_start: 0.7296 (mt0) cc_final: 0.6904 (mt0) REVERT: C 943 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7789 (mm) REVERT: C 963 GLU cc_start: 0.6488 (tt0) cc_final: 0.5814 (mm-30) REVERT: C 1012 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7680 (m170) REVERT: C 1023 LEU cc_start: 0.7973 (mt) cc_final: 0.7733 (mm) outliers start: 105 outliers final: 66 residues processed: 608 average time/residue: 1.1379 time to fit residues: 821.0955 Evaluate side-chains 632 residues out of total 2588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 537 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 568 GLU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 816 ARG Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 608 GLU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 724 ASP Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 816 ARG Chi-restraints excluded: chain C residue 818 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 975 THR Chi-restraints excluded: chain C residue 1004 THR Chi-restraints excluded: chain C residue 1012 HIS Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN B 108 GLN B 112 GLN B 384 ASN C 148 ASN C 274 ASN C 531 ASN C 598 ASN ** C 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 795 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C1012 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.163272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.133180 restraints weight = 25623.639| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.24 r_work: 0.3149 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24442 Z= 0.156 Angle : 0.599 23.782 33247 Z= 0.281 Chirality : 0.052 2.053 3913 Planarity : 0.004 0.052 4261 Dihedral : 5.698 103.318 3354 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.94 % Allowed : 21.29 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.15), residues: 3134 helix: 2.33 (0.12), residues: 1689 sheet: 0.50 (0.24), residues: 432 loop : -0.13 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 755 HIS 0.007 0.001 HIS A 342 PHE 0.024 0.001 PHE A 380 TYR 0.014 0.001 TYR B 327 ARG 0.006 0.000 ARG B 8 =============================================================================== Job complete usr+sys time: 11353.77 seconds wall clock time: 201 minutes 7.49 seconds (12067.49 seconds total)