Starting phenix.real_space_refine on Sat Aug 23 16:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wla_37614/08_2025/8wla_37614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wla_37614/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wla_37614/08_2025/8wla_37614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wla_37614/08_2025/8wla_37614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wla_37614/08_2025/8wla_37614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wla_37614/08_2025/8wla_37614.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'TYR:plan': 3, 'TRP:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 2.41, per 1000 atoms: 0.18 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: 1.08 Conformation dependent library (CDL) restraints added in 459.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 2.13 Time building geometry restraints manager: 1.46 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: 1.090 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- 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 : 5.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.003 0.001 ARG B 520 TYR 0.012 0.001 TYR B1093 PHE 0.027 0.002 PHE B1489 TRP 0.011 0.001 TRP B1354 HIS 0.003 0.001 HIS B1294 Details of bonding type rmsd covalent geometry : bond 0.00323 (13704) covalent geometry : angle 0.55839 (18612) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.94043 ( 4) hydrogen bonds : bond 0.13523 ( 801) hydrogen bonds : angle 5.53889 ( 2334) *********************** 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 : 0.464 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: 0.1056 time to fit residues: 31.4675 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 : 0.381 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.196001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.156244 restraints weight = 24004.311| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.47 r_work: 0.3825 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1160 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13706 Z= 0.153 Angle : 0.624 7.865 18616 Z= 0.324 Chirality : 0.042 0.152 2066 Planarity : 0.005 0.043 2356 Dihedral : 4.580 59.410 1830 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.12 % Allowed : 12.16 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.21), residues: 1642 helix: 2.27 (0.16), residues: 1003 sheet: 1.17 (0.60), residues: 82 loop : -0.48 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1182 TYR 0.021 0.002 TYR B1517 PHE 0.038 0.002 PHE B 186 TRP 0.017 0.002 TRP B 884 HIS 0.005 0.001 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00318 (13704) covalent geometry : angle 0.62417 (18612) SS BOND : bond 0.00273 ( 2) SS BOND : angle 1.41955 ( 4) hydrogen bonds : bond 0.04545 ( 801) hydrogen bonds : angle 4.53831 ( 2334) *********************** 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 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 PRO cc_start: 0.5868 (Cg_endo) cc_final: 0.5657 (Cg_exo) REVERT: B 175 LEU cc_start: 0.1381 (mt) cc_final: 0.0525 (mt) REVERT: B 320 PHE cc_start: 0.4273 (m-80) cc_final: 0.3602 (m-80) REVERT: B 431 TRP cc_start: 0.3607 (m100) cc_final: 0.3249 (m-90) REVERT: B 656 MET cc_start: 0.0065 (OUTLIER) cc_final: -0.1534 (ptp) REVERT: B 698 ILE cc_start: 0.2523 (mt) cc_final: 0.2093 (mt) REVERT: B 883 GLU cc_start: 0.6530 (mp0) cc_final: 0.4694 (tt0) REVERT: B 942 TRP cc_start: 0.3598 (t60) cc_final: 0.3155 (t60) REVERT: B 1317 ASN cc_start: 0.0929 (m-40) cc_final: -0.0190 (t0) REVERT: B 1327 MET cc_start: 0.4320 (ptt) cc_final: 0.3501 (tpt) REVERT: B 1438 PHE cc_start: 0.4194 (t80) cc_final: 0.3811 (t80) REVERT: B 1452 MET cc_start: 0.3661 (mpp) cc_final: 0.1198 (mmm) REVERT: B 1499 PHE cc_start: 0.1004 (t80) cc_final: -0.0837 (t80) REVERT: B 1796 MET cc_start: 0.5630 (ptt) cc_final: 0.5193 (mmm) outliers start: 30 outliers final: 17 residues processed: 178 average time/residue: 0.0972 time to fit residues: 26.0219 Evaluate side-chains 143 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1010 PHE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1328 CYS Chi-restraints excluded: chain B residue 1467 HIS 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 154 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 37 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 B1490 ASN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.208082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.168309 restraints weight = 23203.536| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.85 r_work: 0.4091 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1143 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13706 Z= 0.132 Angle : 0.571 7.805 18616 Z= 0.295 Chirality : 0.040 0.203 2066 Planarity : 0.004 0.052 2356 Dihedral : 4.387 46.496 1830 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.91 % Allowed : 13.07 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.21), residues: 1642 helix: 2.06 (0.16), residues: 1011 sheet: 1.24 (0.59), residues: 82 loop : -0.56 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 179 TYR 0.020 0.002 TYR B 148 PHE 0.027 0.002 PHE B1489 TRP 0.029 0.002 TRP B 695 HIS 0.022 0.002 HIS B1767 Details of bonding type rmsd covalent geometry : bond 0.00268 (13704) covalent geometry : angle 0.57050 (18612) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.42331 ( 4) hydrogen bonds : bond 0.04086 ( 801) hydrogen bonds : angle 4.39780 ( 2334) *********************** 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 158 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.0161 (ptp) cc_final: -0.0061 (ppp) REVERT: B 147 PRO cc_start: 0.5558 (Cg_endo) cc_final: 0.5355 (Cg_exo) REVERT: B 175 LEU cc_start: 0.1152 (mt) cc_final: 0.0803 (mp) REVERT: B 308 TYR cc_start: 0.1245 (t80) cc_final: 0.1021 (t80) REVERT: B 320 PHE cc_start: 0.4147 (m-80) cc_final: 0.3584 (m-80) REVERT: B 656 MET cc_start: 0.0767 (mtm) cc_final: -0.2256 (ttt) REVERT: B 883 GLU cc_start: 0.6203 (mp0) cc_final: 0.4433 (tt0) REVERT: B 958 MET cc_start: 0.2237 (tpt) cc_final: 0.2003 (ptp) REVERT: B 1235 ARG cc_start: 0.1171 (mmm-85) cc_final: 0.0945 (mmm160) REVERT: B 1327 MET cc_start: 0.4315 (ptt) cc_final: 0.3945 (tpt) REVERT: B 1796 MET cc_start: 0.5832 (ptt) cc_final: 0.5486 (mmt) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.0963 time to fit residues: 22.0932 Evaluate side-chains 136 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 536 CYS 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 826 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 982 ASN Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1070 VAL Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1439 SER Chi-restraints excluded: chain B residue 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE 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 116 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 105 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1767 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.209979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.171188 restraints weight = 23077.019| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.89 r_work: 0.4117 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1264 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13706 Z= 0.126 Angle : 0.580 13.554 18616 Z= 0.289 Chirality : 0.040 0.241 2066 Planarity : 0.004 0.044 2356 Dihedral : 4.119 20.264 1827 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.05 % Allowed : 14.98 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1642 helix: 2.07 (0.16), residues: 1012 sheet: 0.77 (0.54), residues: 90 loop : -0.50 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 179 TYR 0.034 0.001 TYR A 79 PHE 0.027 0.001 PHE B1489 TRP 0.018 0.001 TRP B 884 HIS 0.009 0.001 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00257 (13704) covalent geometry : angle 0.57903 (18612) SS BOND : bond 0.00692 ( 2) SS BOND : angle 2.37359 ( 4) hydrogen bonds : bond 0.03740 ( 801) hydrogen bonds : angle 4.31063 ( 2334) *********************** 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 153 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 LEU cc_start: 0.1347 (mt) cc_final: 0.1125 (mp) REVERT: B 320 PHE cc_start: 0.4468 (m-80) cc_final: 0.3838 (m-80) REVERT: B 656 MET cc_start: 0.0661 (mtm) cc_final: -0.1156 (tpt) REVERT: B 958 MET cc_start: 0.2487 (tpt) cc_final: 0.2160 (ptp) REVERT: B 1327 MET cc_start: 0.4769 (ptt) cc_final: 0.3805 (ttm) REVERT: B 1556 HIS cc_start: 0.3324 (OUTLIER) cc_final: 0.2541 (t70) outliers start: 29 outliers final: 16 residues processed: 144 average time/residue: 0.0839 time to fit residues: 18.6235 Evaluate side-chains 130 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 522 TRP 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 1010 PHE Chi-restraints excluded: chain B residue 1199 ILE 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 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1669 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- 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** B1099 GLN B1107 ASN B1469 GLN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.212218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.174734 restraints weight = 23570.258| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.89 r_work: 0.4175 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1296 moved from start: 0.4188 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= 0.125 Angle : 0.582 9.717 18616 Z= 0.292 Chirality : 0.041 0.247 2066 Planarity : 0.004 0.034 2356 Dihedral : 4.089 19.526 1827 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.91 % Allowed : 14.91 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1642 helix: 1.96 (0.16), residues: 1020 sheet: 0.96 (0.55), residues: 85 loop : -0.57 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.032 0.001 TYR A 79 PHE 0.035 0.001 PHE A 44 TRP 0.020 0.002 TRP B 884 HIS 0.023 0.001 HIS B1767 Details of bonding type rmsd covalent geometry : bond 0.00266 (13704) covalent geometry : angle 0.58039 (18612) SS BOND : bond 0.00368 ( 2) SS BOND : angle 2.53216 ( 4) hydrogen bonds : bond 0.03626 ( 801) hydrogen bonds : angle 4.28680 ( 2334) *********************** 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 151 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.489 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 190 MET cc_start: 0.3147 (ptt) cc_final: 0.2903 (mtt) REVERT: B 656 MET cc_start: 0.0889 (mtm) cc_final: -0.1346 (tpt) REVERT: B 958 MET cc_start: 0.2466 (tpt) cc_final: 0.2172 (ptp) REVERT: B 1288 LEU cc_start: -0.1417 (tp) cc_final: -0.1825 (pp) REVERT: B 1317 ASN cc_start: 0.2006 (m-40) cc_final: 0.0658 (t0) REVERT: B 1327 MET cc_start: 0.4694 (ptt) cc_final: 0.3836 (ttm) REVERT: B 1556 HIS cc_start: 0.2885 (OUTLIER) cc_final: 0.2292 (t70) outliers start: 27 outliers final: 18 residues processed: 139 average time/residue: 0.0906 time to fit residues: 19.4764 Evaluate side-chains 134 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 431 TRP Chi-restraints excluded: chain B residue 522 TRP 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 1010 PHE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1199 ILE 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 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1669 PHE Chi-restraints excluded: chain B residue 1752 ILE 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 93 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 59 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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** ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.215954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.181234 restraints weight = 24029.686| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 2.86 r_work: 0.4234 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1524 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13706 Z= 0.139 Angle : 0.591 8.540 18616 Z= 0.303 Chirality : 0.041 0.190 2066 Planarity : 0.004 0.053 2356 Dihedral : 4.201 19.228 1827 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1642 helix: 1.80 (0.16), residues: 1009 sheet: 1.07 (0.54), residues: 85 loop : -0.52 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.026 0.002 TYR A 79 PHE 0.031 0.002 PHE A 44 TRP 0.022 0.002 TRP B 884 HIS 0.040 0.002 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00287 (13704) covalent geometry : angle 0.59110 (18612) SS BOND : bond 0.01081 ( 2) SS BOND : angle 0.68138 ( 4) hydrogen bonds : bond 0.03661 ( 801) hydrogen bonds : angle 4.32091 ( 2334) *********************** 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 165 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LEU cc_start: 0.1284 (OUTLIER) cc_final: 0.0012 (mt) REVERT: B 656 MET cc_start: 0.1491 (mtm) cc_final: -0.1328 (tpt) REVERT: B 1288 LEU cc_start: -0.1417 (tp) cc_final: -0.1833 (tp) REVERT: B 1292 TYR cc_start: 0.2034 (m-80) cc_final: 0.1702 (m-80) REVERT: B 1327 MET cc_start: 0.4704 (ptt) cc_final: 0.3612 (ttm) REVERT: B 1556 HIS cc_start: 0.3834 (OUTLIER) cc_final: 0.2732 (t70) outliers start: 35 outliers final: 21 residues processed: 151 average time/residue: 0.0901 time to fit residues: 21.0031 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 : 0.412 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain B residue 522 TRP 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 794 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 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 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 142 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN B 188 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN B1281 GLN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1748 HIS B1767 HIS B1839 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.222494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.192097 restraints weight = 25224.567| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.92 r_work: 0.4324 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1928 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13706 Z= 0.186 Angle : 0.690 14.383 18616 Z= 0.358 Chirality : 0.045 0.389 2066 Planarity : 0.005 0.067 2356 Dihedral : 4.669 22.621 1827 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.47 % Allowed : 15.97 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.21), residues: 1642 helix: 1.25 (0.16), residues: 1003 sheet: 0.52 (0.54), residues: 90 loop : -0.60 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 179 TYR 0.022 0.002 TYR A 79 PHE 0.025 0.002 PHE B1489 TRP 0.023 0.002 TRP B 884 HIS 0.050 0.002 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00390 (13704) covalent geometry : angle 0.69011 (18612) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.51726 ( 4) hydrogen bonds : bond 0.04137 ( 801) hydrogen bonds : angle 4.72453 ( 2334) *********************** 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 176 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.0839 (ppp) cc_final: 0.0279 (tpt) REVERT: B 190 MET cc_start: 0.4212 (ptt) cc_final: 0.3723 (mtt) REVERT: B 304 HIS cc_start: 0.0060 (m90) cc_final: -0.1179 (m170) REVERT: B 1292 TYR cc_start: 0.2625 (m-80) cc_final: 0.1918 (m-80) REVERT: B 1327 MET cc_start: 0.4480 (ptt) cc_final: 0.3613 (ttm) REVERT: B 1556 HIS cc_start: 0.3987 (OUTLIER) cc_final: 0.2385 (t-170) REVERT: B 1565 ILE cc_start: 0.4071 (tt) cc_final: 0.3832 (mt) REVERT: B 1661 MET cc_start: -0.0279 (ttp) cc_final: -0.1128 (ttp) REVERT: B 1771 LEU cc_start: 0.3695 (tp) cc_final: 0.3468 (tt) outliers start: 35 outliers final: 25 residues processed: 156 average time/residue: 0.1006 time to fit residues: 23.6224 Evaluate side-chains 151 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 522 TRP Chi-restraints excluded: chain B residue 569 MET 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 1025 TYR Chi-restraints excluded: chain B residue 1051 LEU 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 1439 SER Chi-restraints excluded: chain B residue 1462 PHE Chi-restraints excluded: chain B residue 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** B1349 GLN ** B1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1681 GLN B1767 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.224450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.194211 restraints weight = 24978.244| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 2.90 r_work: 0.4378 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1906 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13706 Z= 0.131 Angle : 0.623 13.552 18616 Z= 0.316 Chirality : 0.042 0.260 2066 Planarity : 0.004 0.047 2356 Dihedral : 4.419 20.268 1827 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.05 % Allowed : 16.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.21), residues: 1642 helix: 1.40 (0.16), residues: 1010 sheet: 0.35 (0.53), residues: 90 loop : -0.60 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 598 TYR 0.020 0.001 TYR A 79 PHE 0.026 0.002 PHE A 44 TRP 0.022 0.002 TRP B 884 HIS 0.025 0.002 HIS B1748 Details of bonding type rmsd covalent geometry : bond 0.00278 (13704) covalent geometry : angle 0.62308 (18612) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.41979 ( 4) hydrogen bonds : bond 0.03726 ( 801) hydrogen bonds : angle 4.53098 ( 2334) *********************** 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 157 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.0895 (ppp) cc_final: 0.0173 (tpt) REVERT: B 171 LEU cc_start: 0.1314 (mt) cc_final: 0.0207 (mt) REVERT: B 190 MET cc_start: 0.4019 (ptt) cc_final: 0.3574 (mtt) REVERT: B 304 HIS cc_start: -0.0208 (m90) cc_final: -0.1103 (m170) REVERT: B 754 TRP cc_start: 0.2421 (t-100) cc_final: 0.1770 (t-100) REVERT: B 1199 ILE cc_start: 0.0186 (OUTLIER) cc_final: -0.0052 (mt) REVERT: B 1235 ARG cc_start: 0.2283 (mmm-85) cc_final: 0.1726 (mmm160) REVERT: B 1327 MET cc_start: 0.4427 (ptt) cc_final: 0.3500 (ttm) REVERT: B 1661 MET cc_start: -0.0265 (ttp) cc_final: -0.1022 (ttp) REVERT: B 1771 LEU cc_start: 0.3464 (tp) cc_final: 0.3150 (tt) outliers start: 29 outliers final: 20 residues processed: 146 average time/residue: 0.0888 time to fit residues: 20.1242 Evaluate side-chains 144 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 368 GLN 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 1025 TYR Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1199 ILE Chi-restraints excluded: chain B residue 1287 PHE 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 1556 HIS 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 1748 HIS Chi-restraints excluded: chain B residue 1752 ILE 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 49 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 144 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 B1146 HIS B1518 HIS B1556 HIS B1748 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.228236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.200893 restraints weight = 26241.921| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 2.94 r_work: 0.4453 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2189 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13706 Z= 0.166 Angle : 0.683 14.145 18616 Z= 0.350 Chirality : 0.044 0.289 2066 Planarity : 0.005 0.054 2356 Dihedral : 4.731 22.764 1827 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.84 % Allowed : 16.96 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1642 helix: 1.06 (0.16), residues: 1013 sheet: 0.08 (0.52), residues: 92 loop : -0.77 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 598 TYR 0.028 0.002 TYR B1330 PHE 0.043 0.002 PHE B1010 TRP 0.026 0.002 TRP B 533 HIS 0.036 0.002 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00360 (13704) covalent geometry : angle 0.68308 (18612) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.54936 ( 4) hydrogen bonds : bond 0.04025 ( 801) hydrogen bonds : angle 4.85359 ( 2334) *********************** 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 155 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.0924 (ppp) cc_final: 0.0320 (tpt) REVERT: B 171 LEU cc_start: 0.1594 (mt) cc_final: 0.0487 (mt) REVERT: B 175 LEU cc_start: 0.2180 (mt) cc_final: 0.1837 (mp) REVERT: B 190 MET cc_start: 0.4019 (ptt) cc_final: 0.3434 (mtt) REVERT: B 304 HIS cc_start: 0.0812 (m90) cc_final: 0.0015 (m170) REVERT: B 1327 MET cc_start: 0.4482 (ptt) cc_final: 0.3692 (ttm) REVERT: B 1462 PHE cc_start: 0.2916 (t80) cc_final: 0.1887 (m-10) REVERT: B 1661 MET cc_start: -0.0052 (ttp) cc_final: -0.0874 (ttp) outliers start: 26 outliers final: 21 residues processed: 147 average time/residue: 0.0944 time to fit residues: 21.3522 Evaluate side-chains 143 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 357 VAL 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 1047 ILE Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1287 PHE 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 1452 MET Chi-restraints excluded: chain B residue 1556 HIS Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 1 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 HIS ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1086 GLN B1214 GLN B1347 ASN ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1748 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.238691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.217470 restraints weight = 27851.274| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 3.04 r_work: 0.4658 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3067 moved from start: 0.9675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 13706 Z= 0.293 Angle : 1.039 18.941 18616 Z= 0.543 Chirality : 0.063 1.065 2066 Planarity : 0.007 0.074 2356 Dihedral : 6.253 31.406 1827 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.05 % Allowed : 17.31 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.20), residues: 1642 helix: -0.27 (0.15), residues: 1011 sheet: -0.60 (0.58), residues: 84 loop : -1.29 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 988 TYR 0.043 0.004 TYR B 423 PHE 0.043 0.004 PHE B 606 TRP 0.038 0.004 TRP B 398 HIS 0.051 0.003 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00650 (13704) covalent geometry : angle 1.03875 (18612) SS BOND : bond 0.00666 ( 2) SS BOND : angle 1.73746 ( 4) hydrogen bonds : bond 0.06478 ( 801) hydrogen bonds : angle 6.22329 ( 2334) ********************** 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 201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.5087 (t70) cc_final: 0.4443 (p0) REVERT: B 293 MET cc_start: 0.3161 (mmm) cc_final: 0.2941 (mmm) REVERT: B 671 VAL cc_start: 0.6260 (m) cc_final: 0.5830 (m) REVERT: B 978 MET cc_start: 0.1982 (ptt) cc_final: 0.1746 (mtm) REVERT: B 1040 THR cc_start: 0.2748 (t) cc_final: 0.2324 (m) REVERT: B 1047 ILE cc_start: 0.1461 (OUTLIER) cc_final: 0.1062 (tt) REVERT: B 1230 MET cc_start: 0.0555 (ppp) cc_final: 0.0087 (ppp) REVERT: B 1327 MET cc_start: 0.4402 (ptt) cc_final: 0.3439 (ttm) REVERT: B 1353 ASP cc_start: 0.6787 (m-30) cc_final: 0.6480 (m-30) REVERT: B 1457 MET cc_start: -0.1391 (mmt) cc_final: -0.2668 (mtm) REVERT: B 1582 ILE cc_start: -0.2336 (OUTLIER) cc_final: -0.2572 (tt) REVERT: B 1661 MET cc_start: 0.1233 (ttp) cc_final: 0.0533 (ttp) outliers start: 29 outliers final: 19 residues processed: 192 average time/residue: 0.0825 time to fit residues: 24.9855 Evaluate side-chains 178 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR 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 565 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1205 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1287 PHE Chi-restraints excluded: chain B residue 1321 LEU Chi-restraints excluded: chain B residue 1328 CYS Chi-restraints excluded: chain B residue 1347 ASN Chi-restraints excluded: chain B residue 1348 PHE Chi-restraints excluded: chain B residue 1452 MET Chi-restraints excluded: chain B residue 1576 PHE Chi-restraints excluded: chain B residue 1582 ILE Chi-restraints excluded: chain B residue 1752 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 10 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1087 ASN B1099 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1347 ASN ** B1349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1556 HIS B1767 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.237681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.217591 restraints weight = 28780.854| |-----------------------------------------------------------------------------| r_work (start): 0.4696 rms_B_bonded: 2.95 r_work: 0.4606 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3053 moved from start: 0.9850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 13706 Z= 0.377 Angle : 1.169 59.196 18616 Z= 0.642 Chirality : 0.067 1.414 2066 Planarity : 0.008 0.111 2356 Dihedral : 6.201 30.459 1827 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 34.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.40 % Allowed : 18.30 % Favored : 79.29 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.20), residues: 1642 helix: -0.36 (0.15), residues: 1014 sheet: -0.71 (0.58), residues: 84 loop : -1.36 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.002 ARG A 73 TYR 0.066 0.004 TYR B1358 PHE 0.052 0.004 PHE B 287 TRP 0.036 0.003 TRP B 398 HIS 0.044 0.003 HIS B1556 Details of bonding type rmsd covalent geometry : bond 0.00800 (13704) covalent geometry : angle 1.16930 (18612) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.52093 ( 4) hydrogen bonds : bond 0.06264 ( 801) hydrogen bonds : angle 6.17012 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.08 seconds wall clock time: 49 minutes 43.10 seconds (2983.10 seconds total)