Starting phenix.real_space_refine on Thu Jul 31 11:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.map" model { file = "/net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wla_37614/07_2025/8wla_37614.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8672 2.51 5 N 2249 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1383 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 169} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 11977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1492, 11977 Classifications: {'peptide': 1492} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 65, 'TRANS': 1426} Chain breaks: 12 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 7.50, per 1000 atoms: 0.56 Number of scatterers: 13360 At special positions: 0 Unit cell: (114.135, 129.353, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2359 8.00 N 2249 7.00 C 8672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B1328 " - pdb=" SG CYS B1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 68.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.931A pdb=" N SER A 78 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.664A pdb=" N LEU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.910A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.657A pdb=" N ASP B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 199 removed outlier: 4.146A pdb=" N ARG B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.779A pdb=" N LEU B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 removed outlier: 4.347A pdb=" N ASN B 316 " --> pdb=" O TRP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.577A pdb=" N GLN B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.952A pdb=" N ILE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 389 through 396 removed outlier: 3.779A pdb=" N LEU B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 418 through 427 removed outlier: 4.548A pdb=" N TYR B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY B 427 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.586A pdb=" N HIS B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 removed outlier: 3.597A pdb=" N TRP B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.671A pdb=" N TYR B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 518 removed outlier: 3.674A pdb=" N LEU B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 551 Proline residue: B 545 - end of helix Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.600A pdb=" N VAL B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 583 Processing helix chain 'B' and resid 589 through 594 removed outlier: 3.511A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 615 through 654 removed outlier: 3.796A pdb=" N TRP B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Proline residue: B 647 - end of helix Processing helix chain 'B' and resid 664 through 670 removed outlier: 4.115A pdb=" N LEU B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS B 669 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 670 " --> pdb=" O ALA B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 670' Processing helix chain 'B' and resid 671 through 712 removed outlier: 4.017A pdb=" N PHE B 689 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 690 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 692 " --> pdb=" O PHE B 688 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 693 " --> pdb=" O PHE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 734 Proline residue: B 727 - end of helix Processing helix chain 'B' and resid 745 through 764 removed outlier: 4.052A pdb=" N LEU B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 775 Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 793 through 799 removed outlier: 4.033A pdb=" N GLN B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 828 removed outlier: 3.549A pdb=" N THR B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 839 Processing helix chain 'B' and resid 856 through 861 Processing helix chain 'B' and resid 871 through 880 Processing helix chain 'B' and resid 880 through 890 removed outlier: 4.005A pdb=" N PHE B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 888 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 902 removed outlier: 4.286A pdb=" N TYR B 901 " --> pdb=" O GLU B 897 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 902 " --> pdb=" O THR B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 932 through 947 Processing helix chain 'B' and resid 949 through 972 removed outlier: 3.586A pdb=" N THR B 953 " --> pdb=" O THR B 949 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 961 " --> pdb=" O PHE B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 980 removed outlier: 4.116A pdb=" N VAL B 976 " --> pdb=" O ASN B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 Processing helix chain 'B' and resid 1006 through 1010 Processing helix chain 'B' and resid 1011 through 1025 Processing helix chain 'B' and resid 1081 through 1091 removed outlier: 3.890A pdb=" N ASN B1085 " --> pdb=" O GLY B1081 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B1089 " --> pdb=" O ASN B1085 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B1091 " --> pdb=" O ASN B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1114 removed outlier: 3.728A pdb=" N LYS B1114 " --> pdb=" O GLU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1121 Processing helix chain 'B' and resid 1138 through 1142 Processing helix chain 'B' and resid 1177 through 1189 Processing helix chain 'B' and resid 1201 through 1207 Processing helix chain 'B' and resid 1222 through 1233 Processing helix chain 'B' and resid 1267 through 1271 Processing helix chain 'B' and resid 1272 through 1282 Processing helix chain 'B' and resid 1283 through 1294 Processing helix chain 'B' and resid 1294 through 1325 removed outlier: 4.467A pdb=" N HIS B1298 " --> pdb=" O HIS B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1377 Proline residue: B1372 - end of helix removed outlier: 3.631A pdb=" N GLU B1377 " --> pdb=" O ILE B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1446 Processing helix chain 'B' and resid 1449 through 1467 Processing helix chain 'B' and resid 1469 through 1490 removed outlier: 3.984A pdb=" N LEU B1473 " --> pdb=" O GLN B1469 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B1474 " --> pdb=" O ALA B1470 " (cutoff:3.500A) Proline residue: B1486 - end of helix Processing helix chain 'B' and resid 1495 through 1512 Processing helix chain 'B' and resid 1521 through 1534 Processing helix chain 'B' and resid 1556 through 1583 Proline residue: B1567 - end of helix Processing helix chain 'B' and resid 1597 through 1623 Proline residue: B1609 - end of helix Processing helix chain 'B' and resid 1641 through 1665 Processing helix chain 'B' and resid 1668 through 1696 removed outlier: 3.805A pdb=" N MET B1672 " --> pdb=" O ASN B1668 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B1696 " --> pdb=" O ALA B1692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1725 through 1760 Proline residue: B1756 - end of helix Processing helix chain 'B' and resid 1763 through 1774 Processing helix chain 'B' and resid 1786 through 1825 Proline residue: B1818 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 53 removed outlier: 6.374A pdb=" N LEU A 13 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 12 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU A 86 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 14 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N CYS A 88 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 16 " --> pdb=" O CYS A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 373 Processing sheet with id=AA3, first strand: chain 'B' and resid 1068 through 1072 removed outlier: 3.808A pdb=" N PHE B1068 " --> pdb=" O LEU B1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B1047 " --> pdb=" O LEU B1072 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B1033 " --> pdb=" O MET B1004 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 842 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B1001 " --> pdb=" O PHE B 842 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 844 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER B1003 " --> pdb=" O VAL B 844 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 846 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA B1149 " --> pdb=" O ASN B1200 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B1235 " --> pdb=" O VAL B1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1105 through 1106 removed outlier: 3.623A pdb=" N ASP B1106 " --> pdb=" O GLY B1245 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B1245 " --> pdb=" O ASP B1106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 801 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4251 1.34 - 1.46: 3405 1.46 - 1.58: 5924 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 13704 Sorted by residual: bond pdb=" N ARG A 11 " pdb=" CA ARG A 11 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.25e-02 6.40e+03 5.87e+00 bond pdb=" N GLU B 863 " pdb=" CA GLU B 863 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.27e-02 6.20e+03 3.96e+00 bond pdb=" N ILE A 9 " pdb=" CA ILE A 9 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.62e+00 bond pdb=" N ARG A 10 " pdb=" CA ARG A 10 " ideal model delta sigma weight residual 1.463 1.487 -0.024 1.31e-02 5.83e+03 3.44e+00 bond pdb=" C ILE B1436 " pdb=" N PRO B1437 " ideal model delta sigma weight residual 1.335 1.349 -0.014 8.70e-03 1.32e+04 2.43e+00 ... (remaining 13699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18367 1.94 - 3.88: 210 3.88 - 5.82: 29 5.82 - 7.76: 5 7.76 - 9.69: 1 Bond angle restraints: 18612 Sorted by residual: angle pdb=" N ARG B 657 " pdb=" CA ARG B 657 " pdb=" C ARG B 657 " ideal model delta sigma weight residual 107.70 117.39 -9.69 2.09e+00 2.29e-01 2.15e+01 angle pdb=" N TYR B 600 " pdb=" CA TYR B 600 " pdb=" CB TYR B 600 " ideal model delta sigma weight residual 110.52 118.13 -7.61 1.65e+00 3.67e-01 2.13e+01 angle pdb=" N CYS B 658 " pdb=" CA CYS B 658 " pdb=" C CYS B 658 " ideal model delta sigma weight residual 109.07 114.97 -5.90 1.52e+00 4.33e-01 1.51e+01 angle pdb=" N MET B 656 " pdb=" CA MET B 656 " pdb=" C MET B 656 " ideal model delta sigma weight residual 110.17 115.70 -5.53 1.51e+00 4.39e-01 1.34e+01 angle pdb=" N ARG B 599 " pdb=" CA ARG B 599 " pdb=" C ARG B 599 " ideal model delta sigma weight residual 111.69 116.07 -4.38 1.23e+00 6.61e-01 1.27e+01 ... (remaining 18607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 7209 16.64 - 33.29: 621 33.29 - 49.93: 173 49.93 - 66.57: 52 66.57 - 83.22: 15 Dihedral angle restraints: 8070 sinusoidal: 3180 harmonic: 4890 Sorted by residual: dihedral pdb=" CD ARG A 10 " pdb=" NE ARG A 10 " pdb=" CZ ARG A 10 " pdb=" NH1 ARG A 10 " ideal model delta sinusoidal sigma weight residual 0.00 -75.76 75.76 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CA ALA B 666 " pdb=" C ALA B 666 " pdb=" N VAL B 667 " pdb=" CA VAL B 667 " ideal model delta harmonic sigma weight residual -180.00 -155.80 -24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE B1841 " pdb=" C PHE B1841 " pdb=" N GLN B1842 " pdb=" CA GLN B1842 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 8067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1593 0.041 - 0.082: 342 0.082 - 0.124: 121 0.124 - 0.165: 7 0.165 - 0.206: 3 Chirality restraints: 2066 Sorted by residual: chirality pdb=" CA ARG B 598 " pdb=" N ARG B 598 " pdb=" C ARG B 598 " pdb=" CB ARG B 598 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA CYS B 658 " pdb=" N CYS B 658 " pdb=" C CYS B 658 " pdb=" CB CYS B 658 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA ILE A 9 " pdb=" N ILE A 9 " pdb=" C ILE A 9 " pdb=" CB ILE A 9 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 2063 not shown) Planarity restraints: 2356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 10 " -1.069 9.50e-02 1.11e+02 4.79e-01 1.39e+02 pdb=" NE ARG A 10 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 10 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 10 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 10 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 11 " -0.569 9.50e-02 1.11e+02 2.55e-01 3.97e+01 pdb=" NE ARG A 11 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 11 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 11 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 11 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 359 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO B 360 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " -0.029 5.00e-02 4.00e+02 ... (remaining 2353 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.02: 2 2.02 - 2.74: 1080 2.74 - 3.46: 20615 3.46 - 4.18: 29856 4.18 - 4.90: 55653 Nonbonded interactions: 107206 Sorted by model distance: nonbonded pdb=" OE2 GLU A 98 " pdb=" O TYR B1517 " model vdw 1.295 3.040 nonbonded pdb=" CB THR B1590 " pdb=" OH TYR B1858 " model vdw 1.953 3.470 nonbonded pdb=" N GLN B 948 " pdb=" OE1 GLN B 948 " model vdw 2.248 3.120 nonbonded pdb=" O ARG B 657 " pdb=" O THR B1586 " model vdw 2.292 3.040 nonbonded pdb=" O TYR B 777 " pdb=" NE2 GLN B 779 " model vdw 2.341 3.120 ... (remaining 107201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13706 Z= 0.152 Angle : 0.559 9.694 18616 Z= 0.310 Chirality : 0.040 0.206 2066 Planarity : 0.012 0.479 2356 Dihedral : 14.616 83.216 4904 Min Nonbonded Distance : 1.295 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.71 % Allowed : 9.68 % Favored : 89.61 % 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: 2.13 (0.21), residues: 1642 helix: 2.44 (0.16), residues: 984 sheet: 0.80 (0.61), residues: 85 loop : -0.32 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1354 HIS 0.003 0.001 HIS B1294 PHE 0.027 0.002 PHE B1489 TYR 0.012 0.001 TYR B1093 ARG 0.003 0.001 ARG B 520 Details of bonding type rmsd hydrogen bonds : bond 0.13523 ( 801) hydrogen bonds : angle 5.53889 ( 2334) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.94043 ( 4) covalent geometry : bond 0.00323 (13704) covalent geometry : angle 0.55839 (18612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 604 GLN cc_start: 0.4619 (mm-40) cc_final: 0.4076 (mm-40) REVERT: B 633 TYR cc_start: 0.1376 (m-80) cc_final: 0.1115 (m-80) REVERT: B 790 LEU cc_start: 0.4544 (tt) cc_final: 0.3064 (mm) REVERT: B 883 GLU cc_start: 0.5332 (mp0) cc_final: 0.3684 (tt0) REVERT: B 1317 ASN cc_start: -0.0164 (m-40) cc_final: -0.0475 (t0) REVERT: B 1328 CYS cc_start: -0.1762 (OUTLIER) cc_final: -0.1989 (t) REVERT: B 1438 PHE cc_start: 0.3121 (t80) cc_final: 0.0738 (t80) REVERT: B 1597 ASN cc_start: 0.0508 (t0) cc_final: 0.0298 (m-40) outliers start: 10 outliers final: 1 residues processed: 206 average time/residue: 0.3004 time to fit residues: 89.0289 Evaluate side-chains 139 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1328 CYS Chi-restraints excluded: chain B residue 1467 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.5980 chunk 125 optimal weight: 0.0000 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 101 GLN A 110 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 ASN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1668 ASN B1767 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.195215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.154953 restraints weight = 23755.156| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.53 r_work: 0.3806 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1091 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13706 Z= 0.149 Angle : 0.614 7.311 18616 Z= 0.319 Chirality : 0.042 0.158 2066 Planarity : 0.005 0.044 2356 Dihedral : 4.520 59.618 1830 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.98 % Allowed : 11.87 % Favored : 86.15 % 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: 2.03 (0.21), residues: 1642 helix: 2.33 (0.16), residues: 1004 sheet: 1.18 (0.60), residues: 82 loop : -0.47 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 151 HIS 0.005 0.001 HIS B1556 PHE 0.037 0.002 PHE B 186 TYR 0.020 0.002 TYR B1517 ARG 0.006 0.001 ARG B1154 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 801) hydrogen bonds : angle 4.54326 ( 2334) SS BOND : bond 0.00914 ( 2) SS BOND : angle 1.46824 ( 4) covalent geometry : bond 0.00306 (13704) covalent geometry : angle 0.61396 (18612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.6752 (m-30) cc_final: 0.5605 (p0) REVERT: B 147 PRO cc_start: 0.5885 (Cg_endo) cc_final: 0.5656 (Cg_exo) REVERT: B 175 LEU cc_start: 0.1426 (mt) cc_final: 0.0600 (mt) REVERT: B 320 PHE cc_start: 0.4020 (m-80) cc_final: 0.3343 (m-80) REVERT: B 431 TRP cc_start: 0.3495 (m100) cc_final: 0.3143 (m-90) REVERT: B 656 MET cc_start: 0.0045 (OUTLIER) cc_final: -0.0788 (ptp) REVERT: B 790 LEU cc_start: 0.5460 (tt) cc_final: 0.5154 (pp) REVERT: B 883 GLU cc_start: 0.6473 (mp0) cc_final: 0.4661 (tt0) REVERT: B 993 MET cc_start: 0.3664 (OUTLIER) cc_final: 0.2610 (mmp) REVERT: B 1317 ASN cc_start: 0.0539 (m-40) cc_final: -0.0323 (t0) REVERT: B 1327 MET cc_start: 0.4256 (ptt) cc_final: 0.3849 (tpt) REVERT: B 1438 PHE cc_start: 0.4069 (t80) cc_final: 0.3637 (t80) REVERT: B 1452 MET cc_start: 0.3661 (mpp) cc_final: 0.1177 (mmm) REVERT: B 1499 PHE cc_start: 0.0937 (t80) cc_final: -0.0887 (t80) REVERT: B 1796 MET cc_start: 0.5421 (ptt) cc_final: 0.5049 (mmm) outliers start: 28 outliers final: 14 residues processed: 176 average time/residue: 0.3280 time to fit residues: 85.1441 Evaluate side-chains 142 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 CYS Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 993 MET Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1752 ILE Chi-restraints excluded: chain B residue 1767 HIS Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 184 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN B1013 HIS B1071 GLN B1099 GLN B1107 ASN B1469 GLN B1490 ASN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 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 = 0.4678 r_free = 0.4678 target = 0.210896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.173209 restraints weight = 23669.623| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.91 r_work: 0.4153 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1405 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13706 Z= 0.167 Angle : 0.637 7.530 18616 Z= 0.332 Chirality : 0.043 0.222 2066 Planarity : 0.005 0.065 2356 Dihedral : 4.394 22.319 1827 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.40 % Allowed : 12.86 % Favored : 84.73 % 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: 1.51 (0.21), residues: 1642 helix: 1.83 (0.16), residues: 1014 sheet: 1.09 (0.58), residues: 85 loop : -0.58 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 695 HIS 0.034 0.002 HIS B1767 PHE 0.027 0.002 PHE B1489 TYR 0.024 0.002 TYR B 148 ARG 0.010 0.001 ARG B1116 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 801) hydrogen bonds : angle 4.59190 ( 2334) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.96491 ( 4) covalent geometry : bond 0.00350 (13704) covalent geometry : angle 0.63624 (18612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.0195 (ptp) cc_final: -0.0028 (ppp) REVERT: B 175 LEU cc_start: 0.1135 (mt) cc_final: 0.0189 (mp) REVERT: B 319 ARG cc_start: 0.3553 (mtm-85) cc_final: 0.3076 (tpm170) REVERT: B 340 LEU cc_start: 0.1720 (OUTLIER) cc_final: 0.0494 (mp) REVERT: B 656 MET cc_start: 0.1397 (mtm) cc_final: -0.0901 (mtp) REVERT: B 754 TRP cc_start: 0.1699 (t-100) cc_final: 0.1433 (t-100) REVERT: B 880 HIS cc_start: 0.6935 (m-70) cc_final: 0.6496 (m-70) REVERT: B 883 GLU cc_start: 0.6504 (mp0) cc_final: 0.4523 (tt0) REVERT: B 958 MET cc_start: 0.2340 (tpt) cc_final: 0.2098 (ptp) REVERT: B 1327 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4186 (ttm) REVERT: B 1661 MET cc_start: -0.0339 (ttp) cc_final: -0.0919 (ttp) REVERT: B 1796 MET cc_start: 0.6068 (ptt) cc_final: 0.5664 (mmt) outliers start: 34 outliers final: 20 residues processed: 162 average time/residue: 0.2593 time to fit residues: 63.8540 Evaluate side-chains 144 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 522 TRP Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1327 MET Chi-restraints excluded: chain B residue 1347 ASN Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1748 HIS Chi-restraints excluded: chain B residue 1770 MET Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 121 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 0.0030 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1281 GLN ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 HIS B1839 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.216885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.182925 restraints weight = 24264.346| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.89 r_work: 0.4246 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1697 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13706 Z= 0.170 Angle : 0.661 13.590 18616 Z= 0.337 Chirality : 0.043 0.194 2066 Planarity : 0.005 0.081 2356 Dihedral : 4.584 20.000 1827 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 2.69 % Allowed : 14.84 % Favored : 82.47 % 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: 1.08 (0.21), residues: 1642 helix: 1.51 (0.16), residues: 1003 sheet: 0.76 (0.55), residues: 89 loop : -0.73 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 464 HIS 0.010 0.001 HIS B1767 PHE 0.029 0.002 PHE B1489 TYR 0.031 0.002 TYR A 79 ARG 0.008 0.001 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 801) hydrogen bonds : angle 4.60099 ( 2334) SS BOND : bond 0.01430 ( 2) SS BOND : angle 1.17720 ( 4) covalent geometry : bond 0.00358 (13704) covalent geometry : angle 0.66098 (18612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.2041 (mt) cc_final: 0.0907 (mp) REVERT: B 175 LEU cc_start: 0.1416 (mt) cc_final: 0.0356 (mt) REVERT: B 340 LEU cc_start: 0.1341 (OUTLIER) cc_final: 0.0152 (mt) REVERT: B 552 TYR cc_start: 0.6134 (t80) cc_final: 0.5783 (t80) REVERT: B 656 MET cc_start: 0.1154 (mtm) cc_final: -0.1135 (tpt) REVERT: B 684 ASP cc_start: 0.3982 (m-30) cc_final: 0.3566 (m-30) REVERT: B 754 TRP cc_start: 0.2259 (t-100) cc_final: 0.1678 (t-100) REVERT: B 1288 LEU cc_start: -0.1477 (tp) cc_final: -0.2368 (pp) REVERT: B 1292 TYR cc_start: 0.2162 (m-80) cc_final: 0.1609 (m-80) REVERT: B 1556 HIS cc_start: 0.5180 (m90) cc_final: 0.3624 (m-70) REVERT: B 1661 MET cc_start: -0.0284 (ttp) cc_final: -0.0712 (ttp) REVERT: B 1796 MET cc_start: 0.6167 (ptt) cc_final: 0.5924 (mmp) outliers start: 38 outliers final: 27 residues processed: 161 average time/residue: 0.2977 time to fit residues: 75.8604 Evaluate side-chains 144 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 522 TRP Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1328 CYS Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1588 VAL Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1686 ILE Chi-restraints excluded: chain B residue 1748 HIS Chi-restraints excluded: chain B residue 1752 ILE Chi-restraints excluded: chain B residue 1767 HIS Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1469 GLN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1748 HIS B1767 HIS B1838 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.218005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.184582 restraints weight = 24445.878| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.93 r_work: 0.4270 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1679 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13706 Z= 0.130 Angle : 0.602 10.859 18616 Z= 0.303 Chirality : 0.041 0.236 2066 Planarity : 0.004 0.036 2356 Dihedral : 4.334 19.443 1827 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.76 % Allowed : 15.76 % Favored : 81.48 % 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: 1.21 (0.21), residues: 1642 helix: 1.63 (0.16), residues: 1005 sheet: 0.77 (0.55), residues: 88 loop : -0.71 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 464 HIS 0.019 0.001 HIS B1767 PHE 0.032 0.002 PHE A 44 TYR 0.030 0.001 TYR A 79 ARG 0.007 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 801) hydrogen bonds : angle 4.43051 ( 2334) SS BOND : bond 0.00840 ( 2) SS BOND : angle 0.33454 ( 4) covalent geometry : bond 0.00276 (13704) covalent geometry : angle 0.60228 (18612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.1752 (mt) cc_final: 0.0520 (mt) REVERT: B 175 LEU cc_start: 0.1519 (mt) cc_final: 0.0400 (mt) REVERT: B 190 MET cc_start: 0.3989 (ptt) cc_final: 0.3392 (mtt) REVERT: B 552 TYR cc_start: 0.6057 (t80) cc_final: 0.5698 (t80) REVERT: B 656 MET cc_start: 0.1620 (mtm) cc_final: -0.0647 (mtp) REVERT: B 726 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5669 (mt) REVERT: B 754 TRP cc_start: 0.2317 (t-100) cc_final: 0.1894 (t-100) REVERT: B 1288 LEU cc_start: -0.1746 (tp) cc_final: -0.2296 (tp) REVERT: B 1292 TYR cc_start: 0.2134 (m-80) cc_final: 0.1647 (m-80) REVERT: B 1556 HIS cc_start: 0.5226 (m90) cc_final: 0.3731 (m-70) REVERT: B 1661 MET cc_start: -0.0432 (ttp) cc_final: -0.0776 (ttp) outliers start: 39 outliers final: 26 residues processed: 146 average time/residue: 0.2172 time to fit residues: 50.5750 Evaluate side-chains 141 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1025 TYR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1588 VAL Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1748 HIS Chi-restraints excluded: chain B residue 1752 ILE Chi-restraints excluded: chain B residue 1838 HIS Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 HIS B1838 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.221338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.190043 restraints weight = 24753.148| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.90 r_work: 0.4324 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1840 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13706 Z= 0.137 Angle : 0.611 9.163 18616 Z= 0.311 Chirality : 0.042 0.205 2066 Planarity : 0.004 0.041 2356 Dihedral : 4.387 19.969 1827 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.76 % Allowed : 15.90 % Favored : 81.34 % 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: 1.19 (0.21), residues: 1642 helix: 1.58 (0.16), residues: 1013 sheet: 0.62 (0.54), residues: 88 loop : -0.67 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 464 HIS 0.034 0.002 HIS B1838 PHE 0.031 0.002 PHE A 44 TYR 0.027 0.001 TYR A 79 ARG 0.007 0.000 ARG B 657 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 801) hydrogen bonds : angle 4.46628 ( 2334) SS BOND : bond 0.00462 ( 2) SS BOND : angle 1.45322 ( 4) covalent geometry : bond 0.00288 (13704) covalent geometry : angle 0.61050 (18612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.1632 (mt) cc_final: 0.0334 (mt) REVERT: B 175 LEU cc_start: 0.1564 (mt) cc_final: 0.0439 (mt) REVERT: B 190 MET cc_start: 0.4059 (ptt) cc_final: 0.3516 (mtt) REVERT: B 232 MET cc_start: 0.0996 (ppp) cc_final: 0.0323 (ptm) REVERT: B 293 MET cc_start: -0.0177 (tmm) cc_final: -0.0553 (mmm) REVERT: B 754 TRP cc_start: 0.2597 (t-100) cc_final: 0.2297 (t-100) REVERT: B 1292 TYR cc_start: 0.2191 (m-80) cc_final: 0.1550 (m-80) REVERT: B 1565 ILE cc_start: 0.3942 (tt) cc_final: 0.3726 (mt) REVERT: B 1661 MET cc_start: -0.0152 (ttp) cc_final: -0.0640 (ttp) REVERT: B 1771 LEU cc_start: 0.3498 (tp) cc_final: 0.3193 (tt) outliers start: 39 outliers final: 29 residues processed: 156 average time/residue: 0.2222 time to fit residues: 54.6599 Evaluate side-chains 145 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 536 CYS Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1009 LYS Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1523 ILE Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1748 HIS Chi-restraints excluded: chain B residue 1752 ILE Chi-restraints excluded: chain B residue 1767 HIS Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 115 optimal weight: 0.4980 chunk 163 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 109 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 HIS B1748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.222505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.191621 restraints weight = 24922.980| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 2.89 r_work: 0.4343 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1848 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13706 Z= 0.130 Angle : 0.604 11.701 18616 Z= 0.305 Chirality : 0.042 0.242 2066 Planarity : 0.004 0.044 2356 Dihedral : 4.301 20.787 1827 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.40 % Allowed : 16.68 % Favored : 80.92 % 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 (0.21), residues: 1642 helix: 1.64 (0.16), residues: 1009 sheet: 0.61 (0.53), residues: 88 loop : -0.74 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1773 HIS 0.026 0.001 HIS B1767 PHE 0.026 0.002 PHE A 44 TYR 0.030 0.001 TYR B 968 ARG 0.004 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 801) hydrogen bonds : angle 4.45983 ( 2334) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.64548 ( 4) covalent geometry : bond 0.00264 (13704) covalent geometry : angle 0.60422 (18612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 LEU cc_start: 0.1381 (mt) cc_final: 0.0169 (mt) REVERT: B 175 LEU cc_start: 0.1371 (mt) cc_final: 0.0279 (mt) REVERT: B 190 MET cc_start: 0.3959 (ptt) cc_final: 0.3498 (mtt) REVERT: B 232 MET cc_start: 0.1077 (ppp) cc_final: 0.0750 (ptm) REVERT: B 293 MET cc_start: -0.0249 (tmm) cc_final: -0.0912 (mmm) REVERT: B 304 HIS cc_start: -0.0255 (m170) cc_final: -0.0887 (m170) REVERT: B 401 GLU cc_start: -0.0863 (OUTLIER) cc_final: -0.1781 (pt0) REVERT: B 1292 TYR cc_start: 0.2151 (m-80) cc_final: 0.1552 (m-80) REVERT: B 1661 MET cc_start: -0.0051 (ttp) cc_final: -0.0422 (ttp) REVERT: B 1771 LEU cc_start: 0.3387 (tp) cc_final: 0.3065 (tt) outliers start: 34 outliers final: 22 residues processed: 146 average time/residue: 0.2334 time to fit residues: 52.3405 Evaluate side-chains 136 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1337 THR Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1523 ILE Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1748 HIS Chi-restraints excluded: chain B residue 1752 ILE Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 39 optimal weight: 0.0050 chunk 117 optimal weight: 0.0000 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS B1099 GLN B1107 ASN B1146 HIS ** B1228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.227632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.199484 restraints weight = 25730.382| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.99 r_work: 0.4420 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2161 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13706 Z= 0.170 Angle : 0.665 9.350 18616 Z= 0.338 Chirality : 0.044 0.287 2066 Planarity : 0.005 0.043 2356 Dihedral : 4.566 21.582 1827 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.40 % Allowed : 16.68 % Favored : 80.92 % 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: 0.81 (0.21), residues: 1642 helix: 1.32 (0.16), residues: 1011 sheet: 0.24 (0.53), residues: 88 loop : -0.86 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 464 HIS 0.019 0.002 HIS B1013 PHE 0.031 0.002 PHE B1010 TYR 0.024 0.002 TYR A 79 ARG 0.019 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 801) hydrogen bonds : angle 4.72630 ( 2334) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.51403 ( 4) covalent geometry : bond 0.00344 (13704) covalent geometry : angle 0.66549 (18612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.3283 (tpt) cc_final: 0.1588 (mmt) REVERT: B 175 LEU cc_start: 0.1586 (mt) cc_final: 0.0935 (mp) REVERT: B 190 MET cc_start: 0.3976 (ptt) cc_final: 0.3313 (mtt) REVERT: B 304 HIS cc_start: 0.0381 (m170) cc_final: -0.0314 (m170) REVERT: B 348 MET cc_start: 0.0909 (tpp) cc_final: 0.0609 (tpt) REVERT: B 401 GLU cc_start: -0.1204 (OUTLIER) cc_final: -0.2145 (pt0) REVERT: B 522 TRP cc_start: 0.0833 (t-100) cc_final: 0.0492 (t60) REVERT: B 1462 PHE cc_start: 0.2591 (t80) cc_final: 0.1866 (m-10) outliers start: 34 outliers final: 22 residues processed: 146 average time/residue: 0.2350 time to fit residues: 52.7829 Evaluate side-chains 134 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 949 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1452 MET Chi-restraints excluded: chain B residue 1523 ILE Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1518 HIS B1748 HIS B1767 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.230279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.202621 restraints weight = 25362.681| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.94 r_work: 0.4465 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2128 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13706 Z= 0.128 Angle : 0.629 12.842 18616 Z= 0.314 Chirality : 0.042 0.208 2066 Planarity : 0.005 0.049 2356 Dihedral : 4.433 21.846 1827 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.63 % Allowed : 17.81 % Favored : 80.57 % 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: 0.95 (0.21), residues: 1642 helix: 1.51 (0.16), residues: 1006 sheet: 0.27 (0.51), residues: 91 loop : -0.94 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 625 HIS 0.007 0.001 HIS B1088 PHE 0.028 0.002 PHE B1010 TYR 0.024 0.001 TYR B 968 ARG 0.013 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 801) hydrogen bonds : angle 4.58244 ( 2334) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.40338 ( 4) covalent geometry : bond 0.00273 (13704) covalent geometry : angle 0.62933 (18612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.3274 (tpt) cc_final: 0.1635 (mmt) REVERT: B 175 LEU cc_start: 0.1606 (mt) cc_final: 0.0922 (mp) REVERT: B 190 MET cc_start: 0.3801 (ptt) cc_final: 0.3531 (mtt) REVERT: B 293 MET cc_start: 0.0853 (tmm) cc_final: 0.0204 (tmm) REVERT: B 348 MET cc_start: 0.0908 (tpp) cc_final: 0.0632 (tpt) REVERT: B 401 GLU cc_start: -0.1054 (OUTLIER) cc_final: -0.2067 (pt0) REVERT: B 522 TRP cc_start: 0.1523 (t-100) cc_final: 0.1133 (t60) REVERT: B 1072 LEU cc_start: 0.3426 (mt) cc_final: 0.2838 (mt) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.2930 time to fit residues: 62.9776 Evaluate side-chains 127 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1107 ASN Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1523 ILE Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1767 HIS Chi-restraints excluded: chain B residue 1815 ILE Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 132 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 HIS B1071 GLN B1099 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.231513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.204702 restraints weight = 26333.973| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 3.04 r_work: 0.4471 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2221 moved from start: 0.7785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13706 Z= 0.131 Angle : 0.642 10.122 18616 Z= 0.323 Chirality : 0.042 0.202 2066 Planarity : 0.005 0.072 2356 Dihedral : 4.528 28.310 1827 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.27 % Allowed : 18.45 % Favored : 80.28 % 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: 0.87 (0.21), residues: 1642 helix: 1.45 (0.16), residues: 1004 sheet: 0.18 (0.51), residues: 93 loop : -0.97 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 533 HIS 0.012 0.001 HIS B1767 PHE 0.028 0.002 PHE B1010 TYR 0.019 0.001 TYR B 968 ARG 0.012 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 801) hydrogen bonds : angle 4.64312 ( 2334) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.40095 ( 4) covalent geometry : bond 0.00282 (13704) covalent geometry : angle 0.64188 (18612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.3250 (tpt) cc_final: 0.1574 (mmt) REVERT: B 175 LEU cc_start: 0.1584 (mt) cc_final: 0.0819 (mp) REVERT: B 293 MET cc_start: 0.1029 (tmm) cc_final: 0.0145 (tmm) REVERT: B 401 GLU cc_start: -0.1120 (OUTLIER) cc_final: -0.2259 (pt0) REVERT: B 522 TRP cc_start: 0.1398 (t-100) cc_final: 0.1046 (t60) REVERT: B 854 LEU cc_start: 0.3840 (tp) cc_final: 0.3637 (mp) REVERT: B 1043 GLU cc_start: 0.3263 (pt0) cc_final: 0.3010 (pt0) REVERT: B 1462 PHE cc_start: 0.3079 (t80) cc_final: 0.1919 (m-10) REVERT: B 1661 MET cc_start: 0.0539 (ttp) cc_final: 0.0313 (mmm) outliers start: 18 outliers final: 12 residues processed: 127 average time/residue: 0.2189 time to fit residues: 44.3718 Evaluate side-chains 123 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1452 MET Chi-restraints excluded: chain B residue 1523 ILE Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 982 ASN B1099 GLN B1107 ASN B1767 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.238063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.214263 restraints weight = 26795.716| |-----------------------------------------------------------------------------| r_work (start): 0.4670 rms_B_bonded: 3.04 r_work: 0.4566 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2579 moved from start: 0.8947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13706 Z= 0.179 Angle : 0.721 11.261 18616 Z= 0.362 Chirality : 0.046 0.587 2066 Planarity : 0.005 0.056 2356 Dihedral : 4.762 24.006 1827 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 1.55 % Allowed : 18.30 % Favored : 80.14 % 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: 0.44 (0.20), residues: 1642 helix: 1.05 (0.16), residues: 1017 sheet: -0.17 (0.53), residues: 93 loop : -1.03 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 625 HIS 0.005 0.001 HIS B1518 PHE 0.040 0.002 PHE B1010 TYR 0.020 0.002 TYR B 968 ARG 0.010 0.001 ARG B 645 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 801) hydrogen bonds : angle 5.02506 ( 2334) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.41784 ( 4) covalent geometry : bond 0.00369 (13704) covalent geometry : angle 0.72092 (18612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7181.06 seconds wall clock time: 127 minutes 41.70 seconds (7661.70 seconds total)