Starting phenix.real_space_refine on Wed Feb 4 14:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934.map" model { file = "/net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wfp_65934/02_2026/9wfp_65934_trim.cif" } resolution = 4.1 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= 0.002 sd= 0.026 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 54 5.16 5 C 7077 2.51 5 N 1848 2.21 5 O 1964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10943 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10911 Classifications: {'peptide': 1379} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1322} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GDN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.20 Number of scatterers: 10943 At special positions: 0 Unit cell: (90.2, 103.4, 157.3, 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 54 16.00 O 1964 8.00 N 1848 7.00 C 7077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.04 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: 0.90 Conformation dependent library (CDL) restraints added in 594.3 milliseconds 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 61.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.799A pdb=" N TYR A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.544A pdb=" N THR A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.830A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 94 removed outlier: 4.450A pdb=" N TYR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.616A pdb=" N LEU A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 130 removed outlier: 3.828A pdb=" N ALA A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 141 removed outlier: 3.629A pdb=" N TRP A 141 " --> pdb=" O GLU A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 142 through 163 removed outlier: 3.512A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.742A pdb=" N LEU A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.657A pdb=" N LYS A 229 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.623A pdb=" N MET A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.943A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.596A pdb=" N SER A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.808A pdb=" N PHE A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.528A pdb=" N ASN A 312 " --> pdb=" O TRP A 308 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.791A pdb=" N SER A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 4.015A pdb=" N ILE A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 removed outlier: 3.787A pdb=" N VAL A 364 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.522A pdb=" N TYR A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 389 through 404 removed outlier: 6.745A pdb=" N LYS A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 422 through 431 removed outlier: 4.764A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 441 through 453 removed outlier: 3.924A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 485 removed outlier: 3.899A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 Processing helix chain 'A' and resid 496 through 513 removed outlier: 3.678A pdb=" N PHE A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.668A pdb=" N LEU A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 4.246A pdb=" N LEU A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 529 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 4.171A pdb=" N THR A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 557 through 568 removed outlier: 4.622A pdb=" N PHE A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 594 Proline residue: A 574 - end of helix removed outlier: 3.933A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.712A pdb=" N ILE A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 removed outlier: 4.014A pdb=" N PHE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.510A pdb=" N TYR A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 713 " --> pdb=" O TYR A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 removed outlier: 4.211A pdb=" N ASP A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.882A pdb=" N ASN A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.569A pdb=" N SER A 768 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 769 " --> pdb=" O PRO A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 769' Processing helix chain 'A' and resid 775 through 782 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.660A pdb=" N GLY A 788 " --> pdb=" O ARG A 785 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.974A pdb=" N SER A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 837 removed outlier: 4.351A pdb=" N GLU A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 removed outlier: 4.021A pdb=" N LEU A 908 " --> pdb=" O SER A 904 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 909 " --> pdb=" O TRP A 905 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 946 removed outlier: 4.088A pdb=" N MET A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 923 " --> pdb=" O TRP A 919 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS A 927 " --> pdb=" O MET A 923 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 931 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 932 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 978 removed outlier: 3.663A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 962 " --> pdb=" O PHE A 958 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.774A pdb=" N LEU A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 removed outlier: 4.104A pdb=" N PHE A1008 " --> pdb=" O PRO A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 4.020A pdb=" N ILE A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1012 through 1017' Processing helix chain 'A' and resid 1017 through 1022 Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 3.638A pdb=" N VAL A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A1041 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1072 removed outlier: 3.667A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A1061 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Proline residue: A1065 - end of helix removed outlier: 4.265A pdb=" N VAL A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1069 " --> pdb=" O PRO A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1084 through 1092 removed outlier: 3.814A pdb=" N SER A1089 " --> pdb=" O LYS A1085 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1097 removed outlier: 3.505A pdb=" N TYR A1096 " --> pdb=" O ARG A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.932A pdb=" N ASN A1104 " --> pdb=" O GLY A1100 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR A1108 " --> pdb=" O ASN A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1113 No H-bonds generated for 'chain 'A' and resid 1111 through 1113' Processing helix chain 'A' and resid 1115 through 1120 Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1130 through 1147 removed outlier: 3.683A pdb=" N VAL A1135 " --> pdb=" O ARG A1131 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN A1136 " --> pdb=" O PHE A1132 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A1146 " --> pdb=" O TRP A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 removed outlier: 3.839A pdb=" N THR A1158 " --> pdb=" O MET A1154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1163 " --> pdb=" O ALA A1159 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.742A pdb=" N ALA A1176 " --> pdb=" O GLN A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1187 removed outlier: 4.261A pdb=" N TYR A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1192 removed outlier: 3.536A pdb=" N LEU A1192 " --> pdb=" O ILE A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1201 Processing helix chain 'A' and resid 1202 through 1218 removed outlier: 4.217A pdb=" N ALA A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A1212 " --> pdb=" O ASN A1208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A1218 " --> pdb=" O GLY A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1290 Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1344 through 1354 removed outlier: 3.824A pdb=" N SER A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A1352 " --> pdb=" O LEU A1348 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A1353 " --> pdb=" O TRP A1349 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG A1354 " --> pdb=" O GLU A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1362 removed outlier: 3.565A pdb=" N ILE A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1387 Processing helix chain 'A' and resid 1388 through 1395 removed outlier: 3.775A pdb=" N ARG A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1425 removed outlier: 3.955A pdb=" N LEU A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A1422 " --> pdb=" O GLN A1418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 637 through 638 removed outlier: 3.513A pdb=" N SER A 615 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 644 through 645 Processing sheet with id=AA3, first strand: chain 'A' and resid 647 through 648 removed outlier: 5.739A pdb=" N VAL A 648 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS A 812 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 682 Processing sheet with id=AA5, first strand: chain 'A' and resid 1242 through 1243 removed outlier: 3.715A pdb=" N ILE A1242 " --> pdb=" O ILE A1266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1401 through 1402 removed outlier: 3.586A pdb=" N ILE A1432 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY A1273 " --> pdb=" O LYS A1445 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1447 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A1449 " --> pdb=" O VAL A1275 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE A1446 " --> pdb=" O PHE A1457 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A1457 " --> pdb=" O ILE A1446 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL A1448 " --> pdb=" O GLN A1455 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1107 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: 1.80 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1750 1.29 - 1.42: 2917 1.42 - 1.55: 6416 1.55 - 1.68: 9 1.68 - 1.81: 94 Bond restraints: 11186 Sorted by residual: bond pdb=" N4' GDN A1701 " pdb=" O4A GDN A1701 " ideal model delta sigma weight residual 1.209 1.398 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" N2' GDN A1701 " pdb=" O2A GDN A1701 " ideal model delta sigma weight residual 1.207 1.393 -0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" CA SER A 70 " pdb=" C SER A 70 " ideal model delta sigma weight residual 1.522 1.431 0.092 1.40e-02 5.10e+03 4.27e+01 bond pdb=" C SER A 70 " pdb=" O SER A 70 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.29e-02 6.01e+03 3.90e+01 bond pdb=" C ILE A1446 " pdb=" N LEU A1447 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.31e-02 5.83e+03 3.33e+01 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.68: 15055 5.68 - 11.37: 107 11.37 - 17.05: 18 17.05 - 22.74: 4 22.74 - 28.42: 1 Bond angle restraints: 15185 Sorted by residual: angle pdb=" C LEU A 68 " pdb=" CA LEU A 68 " pdb=" CB LEU A 68 " ideal model delta sigma weight residual 111.83 83.41 28.42 1.60e+00 3.91e-01 3.16e+02 angle pdb=" N GLU A1148 " pdb=" CA GLU A1148 " pdb=" C GLU A1148 " ideal model delta sigma weight residual 112.89 133.36 -20.47 1.24e+00 6.50e-01 2.73e+02 angle pdb=" N VAL A 920 " pdb=" CA VAL A 920 " pdb=" C VAL A 920 " ideal model delta sigma weight residual 111.09 130.95 -19.86 1.25e+00 6.40e-01 2.52e+02 angle pdb=" N ARG A 69 " pdb=" CA ARG A 69 " pdb=" C ARG A 69 " ideal model delta sigma weight residual 111.55 93.04 18.51 1.37e+00 5.33e-01 1.82e+02 angle pdb=" N VAL A 973 " pdb=" CA VAL A 973 " pdb=" C VAL A 973 " ideal model delta sigma weight residual 110.36 124.10 -13.74 1.05e+00 9.07e-01 1.71e+02 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 6070 14.88 - 29.75: 460 29.75 - 44.63: 103 44.63 - 59.50: 9 59.50 - 74.38: 13 Dihedral angle restraints: 6655 sinusoidal: 2666 harmonic: 3989 Sorted by residual: dihedral pdb=" C LEU A 68 " pdb=" N LEU A 68 " pdb=" CA LEU A 68 " pdb=" CB LEU A 68 " ideal model delta harmonic sigma weight residual -122.60 -91.24 -31.36 0 2.50e+00 1.60e-01 1.57e+02 dihedral pdb=" C ARG A 71 " pdb=" N ARG A 71 " pdb=" CA ARG A 71 " pdb=" CB ARG A 71 " ideal model delta harmonic sigma weight residual -122.60 -95.28 -27.32 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" N ARG A 69 " pdb=" C ARG A 69 " pdb=" CA ARG A 69 " pdb=" CB ARG A 69 " ideal model delta harmonic sigma weight residual 122.80 96.54 26.26 0 2.50e+00 1.60e-01 1.10e+02 ... (remaining 6652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 1708 0.188 - 0.375: 22 0.375 - 0.563: 3 0.563 - 0.750: 2 0.750 - 0.938: 4 Chirality restraints: 1739 Sorted by residual: chirality pdb=" CA LEU A 972 " pdb=" N LEU A 972 " pdb=" C LEU A 972 " pdb=" CB LEU A 972 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA LEU A1147 " pdb=" N LEU A1147 " pdb=" C LEU A1147 " pdb=" CB LEU A1147 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CA LEU A1150 " pdb=" N LEU A1150 " pdb=" C LEU A1150 " pdb=" CB LEU A1150 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 1736 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GDN A1701 " 0.038 2.00e-02 2.50e+03 4.23e-02 2.24e+01 pdb=" CA2 GDN A1701 " -0.045 2.00e-02 2.50e+03 pdb=" CA3 GDN A1701 " -0.050 2.00e-02 2.50e+03 pdb=" N3 GDN A1701 " 0.055 2.00e-02 2.50e+03 pdb=" O2 GDN A1701 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1446 " 0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C ILE A1446 " -0.081 2.00e-02 2.50e+03 pdb=" O ILE A1446 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A1447 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GDN A1701 " 0.038 2.00e-02 2.50e+03 3.90e-02 1.90e+01 pdb=" CD1 GDN A1701 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GDN A1701 " -0.004 2.00e-02 2.50e+03 pdb=" CA2 GDN A1701 " 0.047 2.00e-02 2.50e+03 pdb=" N2 GDN A1701 " -0.058 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 76 2.58 - 3.16: 9142 3.16 - 3.74: 15990 3.74 - 4.32: 21913 4.32 - 4.90: 33901 Nonbonded interactions: 81022 Sorted by model distance: nonbonded pdb=" O LEU A 68 " pdb=" CB LEU A 68 " model vdw 1.999 2.752 nonbonded pdb=" O ASP A 994 " pdb=" OD1 ASP A 994 " model vdw 2.040 3.040 nonbonded pdb=" O THR A 400 " pdb=" OG1 THR A 404 " model vdw 2.252 3.040 nonbonded pdb=" O LEU A 72 " pdb=" CD2 PHE A 76 " model vdw 2.262 3.340 nonbonded pdb=" O ASP A 263 " pdb=" NH2 ARG A1131 " model vdw 2.318 3.120 ... (remaining 81017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.010 0.189 11187 Z= 0.490 Angle : 1.369 28.422 15187 Z= 0.788 Chirality : 0.084 0.938 1739 Planarity : 0.008 0.086 1914 Dihedral : 11.603 74.376 4082 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 1.09 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 are not related in a simple way. whole: -5.35 (0.17), residues: 1373 helix: -4.21 (0.10), residues: 703 sheet: -1.62 (0.62), residues: 70 loop : -2.76 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 65 TYR 0.030 0.003 TYR A 261 PHE 0.042 0.003 PHE A 302 TRP 0.048 0.004 TRP A 945 HIS 0.014 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.01029 (11186) covalent geometry : angle 1.36891 (15185) SS BOND : bond 0.00421 ( 1) SS BOND : angle 0.92795 ( 2) hydrogen bonds : bond 0.30857 ( 380) hydrogen bonds : angle 10.86177 ( 1107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.435 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: symmetry clash revert: symmetry clash REVERT: A 90 PHE cc_start: 0.8843 (t80) cc_final: 0.8566 (t80) REVERT: A 130 MET cc_start: 0.8847 (mmp) cc_final: 0.8565 (mmm) REVERT: A 141 TRP cc_start: 0.7668 (m100) cc_final: 0.6779 (p-90) REVERT: A 155 MET cc_start: 0.9210 (mmt) cc_final: 0.8956 (ttt) REVERT: A 166 GLU cc_start: 0.8977 (mp0) cc_final: 0.8524 (mp0) REVERT: A 240 SER cc_start: 0.8869 (m) cc_final: 0.8624 (p) REVERT: A 257 LYS cc_start: 0.8539 (tttp) cc_final: 0.8278 (tptt) REVERT: A 402 LEU cc_start: 0.9045 (mp) cc_final: 0.8800 (mp) REVERT: A 421 TRP cc_start: 0.8147 (t60) cc_final: 0.7719 (t-100) REVERT: A 452 MET cc_start: 0.9360 (tmt) cc_final: 0.8985 (tmm) REVERT: A 463 MET cc_start: 0.8847 (ttp) cc_final: 0.8550 (tpp) REVERT: A 535 LEU cc_start: 0.9173 (mp) cc_final: 0.8705 (tt) REVERT: A 561 SER cc_start: 0.9540 (m) cc_final: 0.9162 (t) REVERT: A 572 MET cc_start: 0.8890 (mmm) cc_final: 0.8552 (mmm) REVERT: A 588 LYS cc_start: 0.8650 (mttt) cc_final: 0.8439 (tptt) REVERT: A 746 GLN cc_start: 0.9087 (tp40) cc_final: 0.8062 (tp-100) REVERT: A 747 ARG cc_start: 0.9181 (mtm-85) cc_final: 0.8938 (ptm160) REVERT: A 750 MET cc_start: 0.9327 (mtp) cc_final: 0.9068 (mmm) REVERT: A 923 MET cc_start: 0.9012 (mmt) cc_final: 0.8756 (mmm) REVERT: A 972 LEU cc_start: 0.9253 (mp) cc_final: 0.8945 (tt) REVERT: A 1143 LEU cc_start: 0.9348 (tp) cc_final: 0.9128 (tp) REVERT: A 1289 LEU cc_start: 0.9367 (tp) cc_final: 0.9030 (tt) REVERT: A 1310 PHE cc_start: 0.8431 (m-10) cc_final: 0.7945 (m-80) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1145 time to fit residues: 43.1578 Evaluate side-chains 170 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 331 GLN A 604 ASN A 746 GLN A 800 HIS A 970 GLN A 995 ASN A1128 ASN A1129 ASN A1215 ASN A1383 GLN A1455 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.124841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088720 restraints weight = 27997.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091504 restraints weight = 14891.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093326 restraints weight = 9785.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094497 restraints weight = 7416.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095270 restraints weight = 6205.232| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11187 Z= 0.147 Angle : 0.716 12.565 15187 Z= 0.370 Chirality : 0.045 0.161 1739 Planarity : 0.005 0.053 1914 Dihedral : 7.906 74.757 1516 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.17 % Allowed : 2.27 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -4.17 (0.19), residues: 1373 helix: -2.95 (0.14), residues: 766 sheet: -1.24 (0.60), residues: 71 loop : -2.44 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 69 TYR 0.022 0.002 TYR A 73 PHE 0.024 0.002 PHE A 832 TRP 0.025 0.002 TRP A 121 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00301 (11186) covalent geometry : angle 0.71600 (15185) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.99695 ( 2) hydrogen bonds : bond 0.06178 ( 380) hydrogen bonds : angle 6.22387 ( 1107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8376 (t80) cc_final: 0.8104 (t80) REVERT: A 72 LEU cc_start: 0.8623 (tt) cc_final: 0.7956 (tt) REVERT: A 127 MET cc_start: 0.9492 (tmm) cc_final: 0.9265 (tmm) REVERT: A 130 MET cc_start: 0.8424 (mmp) cc_final: 0.8184 (mmm) REVERT: A 141 TRP cc_start: 0.7302 (m100) cc_final: 0.6706 (p-90) REVERT: A 155 MET cc_start: 0.9177 (mmt) cc_final: 0.8940 (ttt) REVERT: A 183 GLN cc_start: 0.9093 (mt0) cc_final: 0.8457 (mt0) REVERT: A 240 SER cc_start: 0.8735 (m) cc_final: 0.8419 (p) REVERT: A 257 LYS cc_start: 0.8390 (tttp) cc_final: 0.8158 (tptt) REVERT: A 345 SER cc_start: 0.9255 (m) cc_final: 0.8891 (p) REVERT: A 402 LEU cc_start: 0.8992 (mp) cc_final: 0.8705 (mp) REVERT: A 412 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 421 TRP cc_start: 0.8009 (t60) cc_final: 0.7665 (t-100) REVERT: A 467 THR cc_start: 0.9333 (m) cc_final: 0.9047 (p) REVERT: A 535 LEU cc_start: 0.9055 (mp) cc_final: 0.8795 (tt) REVERT: A 746 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8122 (tp-100) REVERT: A 747 ARG cc_start: 0.9246 (mtm-85) cc_final: 0.8819 (ptp-110) REVERT: A 750 MET cc_start: 0.9321 (mtp) cc_final: 0.9005 (mmm) REVERT: A 940 THR cc_start: 0.9264 (m) cc_final: 0.9045 (p) REVERT: A 972 LEU cc_start: 0.9074 (mp) cc_final: 0.8709 (tt) REVERT: A 997 LEU cc_start: 0.9160 (tp) cc_final: 0.8953 (tt) REVERT: A 1106 LEU cc_start: 0.7406 (mt) cc_final: 0.7134 (mt) REVERT: A 1118 MET cc_start: 0.8283 (tpt) cc_final: 0.8017 (tpt) REVERT: A 1143 LEU cc_start: 0.9165 (tp) cc_final: 0.8874 (tp) REVERT: A 1289 LEU cc_start: 0.9451 (tp) cc_final: 0.9160 (tt) REVERT: A 1310 PHE cc_start: 0.8161 (m-10) cc_final: 0.7741 (m-80) REVERT: A 1385 GLN cc_start: 0.8850 (tt0) cc_final: 0.8638 (mt0) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.0841 time to fit residues: 29.8725 Evaluate side-chains 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 456 GLN A 812 HIS ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087382 restraints weight = 28253.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.090179 restraints weight = 15042.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092029 restraints weight = 9862.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093230 restraints weight = 7437.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093812 restraints weight = 6205.668| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11187 Z= 0.143 Angle : 0.646 10.959 15187 Z= 0.329 Chirality : 0.044 0.157 1739 Planarity : 0.004 0.039 1914 Dihedral : 7.057 72.561 1516 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -3.24 (0.21), residues: 1373 helix: -2.02 (0.16), residues: 782 sheet: -1.18 (0.59), residues: 72 loop : -2.26 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 834 TYR 0.025 0.001 TYR A 52 PHE 0.031 0.002 PHE A 832 TRP 0.031 0.001 TRP A 121 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00308 (11186) covalent geometry : angle 0.64616 (15185) SS BOND : bond 0.00281 ( 1) SS BOND : angle 0.89007 ( 2) hydrogen bonds : bond 0.05014 ( 380) hydrogen bonds : angle 5.46360 ( 1107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8668 (t) cc_final: 0.8427 (t) REVERT: A 119 PHE cc_start: 0.7657 (m-80) cc_final: 0.7078 (m-80) REVERT: A 125 MET cc_start: 0.9077 (ttp) cc_final: 0.8760 (ptp) REVERT: A 130 MET cc_start: 0.8479 (mmp) cc_final: 0.8235 (mmm) REVERT: A 141 TRP cc_start: 0.7332 (m100) cc_final: 0.6594 (p-90) REVERT: A 240 SER cc_start: 0.8680 (m) cc_final: 0.8425 (p) REVERT: A 257 LYS cc_start: 0.8407 (tttp) cc_final: 0.8187 (tptt) REVERT: A 345 SER cc_start: 0.9301 (m) cc_final: 0.9083 (t) REVERT: A 402 LEU cc_start: 0.8971 (mp) cc_final: 0.8627 (mp) REVERT: A 403 MET cc_start: 0.8014 (tpt) cc_final: 0.7711 (tpt) REVERT: A 535 LEU cc_start: 0.8971 (mp) cc_final: 0.8745 (tt) REVERT: A 709 TYR cc_start: 0.8597 (t80) cc_final: 0.8315 (t80) REVERT: A 746 GLN cc_start: 0.8955 (tp-100) cc_final: 0.7980 (tp-100) REVERT: A 747 ARG cc_start: 0.9256 (mtm-85) cc_final: 0.8924 (ptp-110) REVERT: A 750 MET cc_start: 0.9230 (mtp) cc_final: 0.8984 (mmm) REVERT: A 961 LEU cc_start: 0.9177 (mm) cc_final: 0.8943 (tt) REVERT: A 972 LEU cc_start: 0.9195 (mp) cc_final: 0.8827 (tt) REVERT: A 1118 MET cc_start: 0.8289 (tpt) cc_final: 0.8039 (tpt) REVERT: A 1175 PHE cc_start: 0.8611 (t80) cc_final: 0.8094 (t80) REVERT: A 1289 LEU cc_start: 0.9459 (tp) cc_final: 0.9167 (tt) REVERT: A 1310 PHE cc_start: 0.8093 (m-10) cc_final: 0.7639 (m-80) REVERT: A 1431 LEU cc_start: 0.9433 (mp) cc_final: 0.9211 (mp) REVERT: A 1436 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7327 (mmm160) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.0740 time to fit residues: 24.0919 Evaluate side-chains 164 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 107 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 183 GLN A 960 ASN A1129 ASN A1287 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088130 restraints weight = 28265.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090882 restraints weight = 15130.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092709 restraints weight = 9987.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093860 restraints weight = 7562.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094646 restraints weight = 6326.615| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11187 Z= 0.133 Angle : 0.624 10.976 15187 Z= 0.314 Chirality : 0.044 0.189 1739 Planarity : 0.004 0.033 1914 Dihedral : 6.444 70.558 1516 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.17 % Allowed : 2.52 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -2.65 (0.22), residues: 1373 helix: -1.45 (0.18), residues: 778 sheet: -0.94 (0.60), residues: 72 loop : -2.18 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 834 TYR 0.027 0.001 TYR A 52 PHE 0.032 0.001 PHE A 832 TRP 0.029 0.001 TRP A 121 HIS 0.007 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00286 (11186) covalent geometry : angle 0.62445 (15185) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.83219 ( 2) hydrogen bonds : bond 0.04283 ( 380) hydrogen bonds : angle 5.08498 ( 1107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8918 (t80) cc_final: 0.8611 (t80) REVERT: A 116 VAL cc_start: 0.8598 (t) cc_final: 0.8335 (t) REVERT: A 119 PHE cc_start: 0.7523 (m-80) cc_final: 0.7015 (m-80) REVERT: A 121 TRP cc_start: 0.9468 (m-10) cc_final: 0.9204 (m-10) REVERT: A 125 MET cc_start: 0.9068 (ttp) cc_final: 0.8759 (ptp) REVERT: A 141 TRP cc_start: 0.7201 (m100) cc_final: 0.6566 (p-90) REVERT: A 174 TYR cc_start: 0.8571 (m-10) cc_final: 0.8338 (m-10) REVERT: A 240 SER cc_start: 0.8478 (m) cc_final: 0.8278 (p) REVERT: A 345 SER cc_start: 0.9249 (m) cc_final: 0.8999 (p) REVERT: A 365 MET cc_start: 0.8623 (mmt) cc_final: 0.8316 (mmt) REVERT: A 402 LEU cc_start: 0.9018 (mp) cc_final: 0.8641 (mp) REVERT: A 403 MET cc_start: 0.7908 (tpt) cc_final: 0.7616 (tpt) REVERT: A 535 LEU cc_start: 0.8978 (mp) cc_final: 0.8705 (tt) REVERT: A 709 TYR cc_start: 0.8626 (t80) cc_final: 0.8368 (t80) REVERT: A 718 LEU cc_start: 0.8921 (tp) cc_final: 0.8702 (tp) REVERT: A 746 GLN cc_start: 0.8889 (tp-100) cc_final: 0.7897 (tp-100) REVERT: A 747 ARG cc_start: 0.9209 (mtm-85) cc_final: 0.8972 (ptp-110) REVERT: A 750 MET cc_start: 0.9210 (mtp) cc_final: 0.8980 (mmm) REVERT: A 961 LEU cc_start: 0.9131 (mm) cc_final: 0.8918 (tt) REVERT: A 972 LEU cc_start: 0.9139 (mp) cc_final: 0.8831 (tt) REVERT: A 1118 MET cc_start: 0.8299 (tpt) cc_final: 0.8099 (tpt) REVERT: A 1175 PHE cc_start: 0.8437 (t80) cc_final: 0.7857 (t80) REVERT: A 1289 LEU cc_start: 0.9465 (tp) cc_final: 0.9165 (tt) REVERT: A 1402 LEU cc_start: 0.8415 (tp) cc_final: 0.8132 (tt) REVERT: A 1436 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7371 (mmm160) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.0850 time to fit residues: 27.2162 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 132 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN A 960 ASN A1129 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.116808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081664 restraints weight = 29249.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083470 restraints weight = 17107.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085300 restraints weight = 10599.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085598 restraints weight = 8671.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.085703 restraints weight = 7583.489| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11187 Z= 0.227 Angle : 0.711 10.538 15187 Z= 0.358 Chirality : 0.046 0.166 1739 Planarity : 0.004 0.052 1914 Dihedral : 6.519 69.834 1516 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.25 % Allowed : 3.36 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -2.27 (0.23), residues: 1373 helix: -1.14 (0.18), residues: 786 sheet: -1.32 (0.69), residues: 60 loop : -1.93 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 834 TYR 0.029 0.002 TYR A 261 PHE 0.027 0.002 PHE A 832 TRP 0.033 0.002 TRP A 421 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00498 (11186) covalent geometry : angle 0.71093 (15185) SS BOND : bond 0.00195 ( 1) SS BOND : angle 0.79800 ( 2) hydrogen bonds : bond 0.04483 ( 380) hydrogen bonds : angle 5.26907 ( 1107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8699 (m-80) cc_final: 0.8349 (m-80) REVERT: A 125 MET cc_start: 0.9125 (ttp) cc_final: 0.8828 (ptp) REVERT: A 174 TYR cc_start: 0.8764 (m-10) cc_final: 0.8518 (m-10) REVERT: A 252 ARG cc_start: 0.8132 (tpt170) cc_final: 0.7845 (tpt170) REVERT: A 365 MET cc_start: 0.8678 (mmt) cc_final: 0.8250 (mmt) REVERT: A 398 LYS cc_start: 0.8986 (pttm) cc_final: 0.8727 (pttm) REVERT: A 402 LEU cc_start: 0.9132 (mp) cc_final: 0.8712 (mp) REVERT: A 403 MET cc_start: 0.8346 (tpt) cc_final: 0.8008 (tpt) REVERT: A 452 MET cc_start: 0.9366 (ppp) cc_final: 0.9161 (ppp) REVERT: A 535 LEU cc_start: 0.9055 (mp) cc_final: 0.8744 (tt) REVERT: A 709 TYR cc_start: 0.8778 (t80) cc_final: 0.8553 (t80) REVERT: A 746 GLN cc_start: 0.8930 (tp-100) cc_final: 0.7886 (tp-100) REVERT: A 747 ARG cc_start: 0.9269 (mtm-85) cc_final: 0.8910 (ptp-110) REVERT: A 750 MET cc_start: 0.9276 (mtp) cc_final: 0.9044 (mmm) REVERT: A 972 LEU cc_start: 0.9133 (mp) cc_final: 0.8923 (tt) REVERT: A 1118 MET cc_start: 0.8444 (tpt) cc_final: 0.8228 (tpt) REVERT: A 1289 LEU cc_start: 0.9466 (tp) cc_final: 0.9176 (tt) REVERT: A 1436 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.7513 (mmm160) outliers start: 3 outliers final: 0 residues processed: 199 average time/residue: 0.0750 time to fit residues: 22.1116 Evaluate side-chains 156 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 119 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 109 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 960 ASN A1129 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.121108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.084706 restraints weight = 28986.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087428 restraints weight = 15468.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089254 restraints weight = 10175.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090412 restraints weight = 7701.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091202 restraints weight = 6440.156| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11187 Z= 0.107 Angle : 0.615 11.204 15187 Z= 0.303 Chirality : 0.042 0.187 1739 Planarity : 0.003 0.041 1914 Dihedral : 6.074 62.925 1516 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.17 % Allowed : 1.43 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -2.05 (0.23), residues: 1373 helix: -0.95 (0.19), residues: 779 sheet: -0.45 (0.66), residues: 72 loop : -1.97 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.026 0.001 TYR A 83 PHE 0.023 0.001 PHE A 90 TRP 0.021 0.001 TRP A 121 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00225 (11186) covalent geometry : angle 0.61534 (15185) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.67694 ( 2) hydrogen bonds : bond 0.03880 ( 380) hydrogen bonds : angle 4.78086 ( 1107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8537 (t80) cc_final: 0.8135 (t80) REVERT: A 83 TYR cc_start: 0.8908 (t80) cc_final: 0.8689 (t80) REVERT: A 121 TRP cc_start: 0.9350 (m-10) cc_final: 0.9100 (m-10) REVERT: A 125 MET cc_start: 0.9059 (ttp) cc_final: 0.8766 (ptp) REVERT: A 173 LEU cc_start: 0.9528 (tt) cc_final: 0.8991 (mm) REVERT: A 241 TRP cc_start: 0.8161 (p-90) cc_final: 0.7898 (p-90) REVERT: A 252 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7794 (tpt170) REVERT: A 365 MET cc_start: 0.8449 (mmt) cc_final: 0.8043 (mmt) REVERT: A 398 LYS cc_start: 0.8911 (pttm) cc_final: 0.8495 (pttm) REVERT: A 402 LEU cc_start: 0.9035 (mp) cc_final: 0.8571 (mp) REVERT: A 403 MET cc_start: 0.8133 (tpt) cc_final: 0.7807 (tpt) REVERT: A 421 TRP cc_start: 0.7799 (t60) cc_final: 0.7064 (t-100) REVERT: A 535 LEU cc_start: 0.9033 (mp) cc_final: 0.8757 (tt) REVERT: A 709 TYR cc_start: 0.8684 (t80) cc_final: 0.8452 (t80) REVERT: A 746 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8006 (tp-100) REVERT: A 747 ARG cc_start: 0.9219 (mtm-85) cc_final: 0.8952 (ptp-110) REVERT: A 972 LEU cc_start: 0.9120 (mp) cc_final: 0.8909 (tt) REVERT: A 1175 PHE cc_start: 0.8422 (t80) cc_final: 0.7852 (t80) REVERT: A 1289 LEU cc_start: 0.9477 (tp) cc_final: 0.9162 (tt) REVERT: A 1402 LEU cc_start: 0.8356 (tp) cc_final: 0.8131 (tt) REVERT: A 1436 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7398 (mmm160) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.0840 time to fit residues: 27.1017 Evaluate side-chains 168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 66 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 94 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085599 restraints weight = 28843.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088371 restraints weight = 15475.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090172 restraints weight = 10187.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091394 restraints weight = 7737.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092210 restraints weight = 6461.846| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11187 Z= 0.100 Angle : 0.613 11.150 15187 Z= 0.297 Chirality : 0.042 0.180 1739 Planarity : 0.003 0.030 1914 Dihedral : 5.837 61.489 1516 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.08 % Allowed : 0.92 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.92 (0.23), residues: 1373 helix: -0.81 (0.19), residues: 783 sheet: -0.31 (0.66), residues: 72 loop : -2.01 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 834 TYR 0.027 0.001 TYR A 52 PHE 0.022 0.001 PHE A 191 TRP 0.019 0.001 TRP A 121 HIS 0.003 0.000 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00209 (11186) covalent geometry : angle 0.61291 (15185) SS BOND : bond 0.00205 ( 1) SS BOND : angle 0.67175 ( 2) hydrogen bonds : bond 0.03548 ( 380) hydrogen bonds : angle 4.53584 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.394 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9035 (ttp) cc_final: 0.8766 (ptp) REVERT: A 130 MET cc_start: 0.8634 (mmp) cc_final: 0.8401 (mmm) REVERT: A 151 LEU cc_start: 0.9026 (mm) cc_final: 0.8701 (mm) REVERT: A 173 LEU cc_start: 0.9534 (tt) cc_final: 0.8984 (mm) REVERT: A 174 TYR cc_start: 0.8669 (m-10) cc_final: 0.8351 (m-10) REVERT: A 257 LYS cc_start: 0.7951 (tppt) cc_final: 0.6889 (tppt) REVERT: A 365 MET cc_start: 0.8380 (mmt) cc_final: 0.7958 (mmt) REVERT: A 398 LYS cc_start: 0.8885 (pttm) cc_final: 0.8430 (pttm) REVERT: A 402 LEU cc_start: 0.9054 (mp) cc_final: 0.8650 (mp) REVERT: A 403 MET cc_start: 0.8125 (tpt) cc_final: 0.7831 (tpt) REVERT: A 421 TRP cc_start: 0.7797 (t60) cc_final: 0.6916 (t-100) REVERT: A 463 MET cc_start: 0.9059 (tpp) cc_final: 0.8572 (tpp) REVERT: A 535 LEU cc_start: 0.9117 (mp) cc_final: 0.8720 (tt) REVERT: A 747 ARG cc_start: 0.9194 (mtm-85) cc_final: 0.8812 (ptp-110) REVERT: A 1083 GLU cc_start: 0.8044 (mp0) cc_final: 0.7331 (tt0) REVERT: A 1175 PHE cc_start: 0.8400 (t80) cc_final: 0.7977 (t80) REVERT: A 1289 LEU cc_start: 0.9457 (tp) cc_final: 0.9191 (tt) REVERT: A 1402 LEU cc_start: 0.8239 (tp) cc_final: 0.8002 (tt) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.0805 time to fit residues: 26.6425 Evaluate side-chains 174 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN A 993 HIS A1129 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.123653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087478 restraints weight = 28430.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090196 restraints weight = 15245.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091988 restraints weight = 10068.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093145 restraints weight = 7648.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093899 restraints weight = 6409.517| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11187 Z= 0.143 Angle : 0.629 11.147 15187 Z= 0.310 Chirality : 0.044 0.178 1739 Planarity : 0.003 0.051 1914 Dihedral : 5.890 61.885 1516 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.08 % Allowed : 1.34 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.72 (0.23), residues: 1373 helix: -0.64 (0.19), residues: 778 sheet: -0.44 (0.65), residues: 72 loop : -1.89 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.020 0.001 TYR A 52 PHE 0.023 0.002 PHE A 968 TRP 0.021 0.002 TRP A 121 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00315 (11186) covalent geometry : angle 0.62916 (15185) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.78477 ( 2) hydrogen bonds : bond 0.03721 ( 380) hydrogen bonds : angle 4.58687 ( 1107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8550 (t80) cc_final: 0.8160 (t80) REVERT: A 130 MET cc_start: 0.8568 (mmp) cc_final: 0.8282 (mmm) REVERT: A 173 LEU cc_start: 0.9519 (tt) cc_final: 0.9001 (mm) REVERT: A 174 TYR cc_start: 0.8598 (m-10) cc_final: 0.8251 (m-10) REVERT: A 398 LYS cc_start: 0.8977 (pttm) cc_final: 0.8650 (pttm) REVERT: A 402 LEU cc_start: 0.8918 (mp) cc_final: 0.8694 (mp) REVERT: A 403 MET cc_start: 0.8001 (tpt) cc_final: 0.7747 (tpt) REVERT: A 463 MET cc_start: 0.9058 (tpp) cc_final: 0.8440 (tpp) REVERT: A 535 LEU cc_start: 0.9084 (mp) cc_final: 0.8695 (tt) REVERT: A 745 LYS cc_start: 0.9492 (mttt) cc_final: 0.9174 (mttm) REVERT: A 746 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8143 (tp-100) REVERT: A 747 ARG cc_start: 0.9189 (mtm-85) cc_final: 0.8629 (ttm-80) REVERT: A 1118 MET cc_start: 0.8453 (tpt) cc_final: 0.8249 (tpt) REVERT: A 1175 PHE cc_start: 0.8355 (t80) cc_final: 0.8076 (t80) REVERT: A 1289 LEU cc_start: 0.9444 (tp) cc_final: 0.9180 (tt) REVERT: A 1402 LEU cc_start: 0.8342 (tp) cc_final: 0.8121 (tt) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.0843 time to fit residues: 26.1303 Evaluate side-chains 161 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN A1129 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088776 restraints weight = 29433.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091525 restraints weight = 15663.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093366 restraints weight = 10269.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094530 restraints weight = 7773.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095275 restraints weight = 6502.805| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11187 Z= 0.132 Angle : 0.630 11.267 15187 Z= 0.310 Chirality : 0.044 0.231 1739 Planarity : 0.003 0.030 1914 Dihedral : 5.816 59.332 1516 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.17 % Allowed : 0.42 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.66 (0.23), residues: 1373 helix: -0.63 (0.19), residues: 789 sheet: -1.04 (0.68), residues: 60 loop : -1.69 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.027 0.001 TYR A 83 PHE 0.021 0.001 PHE A 515 TRP 0.020 0.001 TRP A 121 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00292 (11186) covalent geometry : angle 0.62994 (15185) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.72131 ( 2) hydrogen bonds : bond 0.03703 ( 380) hydrogen bonds : angle 4.67438 ( 1107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8576 (mmp) cc_final: 0.8307 (mmm) REVERT: A 173 LEU cc_start: 0.9503 (tt) cc_final: 0.8983 (mm) REVERT: A 174 TYR cc_start: 0.8603 (m-10) cc_final: 0.8255 (m-10) REVERT: A 398 LYS cc_start: 0.8945 (pttm) cc_final: 0.8645 (pttm) REVERT: A 402 LEU cc_start: 0.8956 (mp) cc_final: 0.8692 (mp) REVERT: A 403 MET cc_start: 0.7982 (tpt) cc_final: 0.7741 (tpt) REVERT: A 535 LEU cc_start: 0.9121 (mp) cc_final: 0.8703 (tt) REVERT: A 709 TYR cc_start: 0.8583 (t80) cc_final: 0.8347 (t80) REVERT: A 745 LYS cc_start: 0.9489 (mttt) cc_final: 0.9178 (mttm) REVERT: A 746 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8173 (tp-100) REVERT: A 747 ARG cc_start: 0.9167 (mtm-85) cc_final: 0.8705 (ttm110) REVERT: A 1289 LEU cc_start: 0.9433 (tp) cc_final: 0.9162 (tt) REVERT: A 1400 LEU cc_start: 0.8356 (tp) cc_final: 0.8056 (tp) REVERT: A 1402 LEU cc_start: 0.8355 (tp) cc_final: 0.8133 (tt) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.0907 time to fit residues: 26.8842 Evaluate side-chains 166 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 HIS A1129 ASN A1166 ASN ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085228 restraints weight = 27288.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086267 restraints weight = 16035.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086803 restraints weight = 10778.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087399 restraints weight = 9882.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087472 restraints weight = 8618.582| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11187 Z= 0.117 Angle : 0.637 11.627 15187 Z= 0.314 Chirality : 0.043 0.225 1739 Planarity : 0.003 0.035 1914 Dihedral : 5.683 59.562 1516 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.58 (0.23), residues: 1373 helix: -0.56 (0.19), residues: 788 sheet: -0.99 (0.68), residues: 60 loop : -1.67 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 834 TYR 0.021 0.001 TYR A 52 PHE 0.024 0.002 PHE A1175 TRP 0.045 0.001 TRP A 121 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00257 (11186) covalent geometry : angle 0.63684 (15185) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.66226 ( 2) hydrogen bonds : bond 0.03684 ( 380) hydrogen bonds : angle 4.66719 ( 1107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.8711 (mmp) cc_final: 0.8357 (mmm) REVERT: A 173 LEU cc_start: 0.9474 (tt) cc_final: 0.8993 (mm) REVERT: A 174 TYR cc_start: 0.8676 (m-10) cc_final: 0.8337 (m-10) REVERT: A 398 LYS cc_start: 0.9036 (pttm) cc_final: 0.8692 (pttm) REVERT: A 402 LEU cc_start: 0.8961 (mp) cc_final: 0.8671 (mp) REVERT: A 403 MET cc_start: 0.8201 (tpt) cc_final: 0.7955 (tpt) REVERT: A 463 MET cc_start: 0.9033 (tpp) cc_final: 0.8644 (tpp) REVERT: A 535 LEU cc_start: 0.9139 (mp) cc_final: 0.8775 (tt) REVERT: A 709 TYR cc_start: 0.8595 (t80) cc_final: 0.8379 (t80) REVERT: A 745 LYS cc_start: 0.9487 (mttt) cc_final: 0.9178 (mttm) REVERT: A 746 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8144 (tp-100) REVERT: A 747 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8619 (ttm-80) REVERT: A 1289 LEU cc_start: 0.9468 (tp) cc_final: 0.9202 (tt) REVERT: A 1400 LEU cc_start: 0.8365 (tp) cc_final: 0.8063 (tp) REVERT: A 1402 LEU cc_start: 0.8249 (tp) cc_final: 0.8020 (tt) REVERT: A 1436 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7363 (mmm160) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.0819 time to fit residues: 24.4529 Evaluate side-chains 155 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 34 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085411 restraints weight = 27071.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087894 restraints weight = 16435.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089007 restraints weight = 9481.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089458 restraints weight = 8501.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089600 restraints weight = 7496.331| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11187 Z= 0.111 Angle : 0.628 11.577 15187 Z= 0.306 Chirality : 0.043 0.241 1739 Planarity : 0.003 0.033 1914 Dihedral : 5.566 57.951 1516 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: -1.48 (0.23), residues: 1373 helix: -0.45 (0.19), residues: 789 sheet: -0.41 (0.64), residues: 72 loop : -1.78 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 834 TYR 0.019 0.001 TYR A 52 PHE 0.023 0.001 PHE A1175 TRP 0.039 0.001 TRP A 121 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00242 (11186) covalent geometry : angle 0.62838 (15185) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.59228 ( 2) hydrogen bonds : bond 0.03589 ( 380) hydrogen bonds : angle 4.61417 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.30 seconds wall clock time: 29 minutes 24.07 seconds (1764.07 seconds total)