Starting phenix.real_space_refine on Thu Nov 20 01:02:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wp6_8871/11_2025/5wp6_8871.map" } resolution = 3.8 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians V 80 8.30 5 S 108 5.16 5 C 18656 2.51 5 N 5104 2.21 5 O 5088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29036 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 977, 7183 Classifications: {'peptide': 977} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 39, 'TRANS': 937} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 606 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 30, 'HIS:plan': 4, 'ARG:plan': 22, 'ASP:plan': 18, 'ASN:plan1': 3, 'GLN:plan1': 11, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 415 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'DVT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 8.49, per 1000 atoms: 0.29 Number of scatterers: 29036 At special positions: 0 Unit cell: (146.88, 146.88, 179.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) V 80 22.97 S 108 16.00 O 5088 8.00 N 5104 7.00 C 18656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7224 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 16 sheets defined 62.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.137A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.550A pdb=" N GLN A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 removed outlier: 3.689A pdb=" N VAL A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 177 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 removed outlier: 3.873A pdb=" N SER A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.897A pdb=" N ARG A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 372 through 384 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.948A pdb=" N LEU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 422 through 435 removed outlier: 4.440A pdb=" N MET A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 4.009A pdb=" N VAL A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG A 442 " --> pdb=" O PRO A 438 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.572A pdb=" N PHE A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.572A pdb=" N LEU A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.627A pdb=" N TRP A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 569 " --> pdb=" O TRP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 4.084A pdb=" N TYR A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 removed outlier: 3.900A pdb=" N SER A 588 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 632 removed outlier: 4.197A pdb=" N ASP A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.650A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.887A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 removed outlier: 4.043A pdb=" N GLN A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.754A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 703 removed outlier: 3.515A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 767 through 776 removed outlier: 3.885A pdb=" N PHE A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 776 " --> pdb=" O TRP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 803 removed outlier: 3.559A pdb=" N ILE A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 835 removed outlier: 4.478A pdb=" N LEU A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.975A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.507A pdb=" N GLN A 866 " --> pdb=" O ASP A 862 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.913A pdb=" N GLY A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 892 " --> pdb=" O TYR A 888 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 897 " --> pdb=" O THR A 893 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 removed outlier: 4.517A pdb=" N ILE A 909 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 911 " --> pdb=" O HIS A 908 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 912 " --> pdb=" O ILE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 925 removed outlier: 3.849A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 953 removed outlier: 4.025A pdb=" N ALA A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A 944 " --> pdb=" O TRP A 940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 953 " --> pdb=" O GLU A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.870A pdb=" N ILE A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 1017 through 1034 removed outlier: 3.799A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1061 removed outlier: 3.734A pdb=" N LYS A1049 " --> pdb=" O TYR A1045 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A1061 " --> pdb=" O TYR A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1072 removed outlier: 4.056A pdb=" N PHE A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A1070 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 3.667A pdb=" N THR A1123 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A1128 " --> pdb=" O TRP A1124 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A1134 " --> pdb=" O GLU A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1163 Processing helix chain 'A' and resid 1165 through 1192 removed outlier: 4.145A pdb=" N GLU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.137A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.550A pdb=" N GLN B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 177 removed outlier: 3.689A pdb=" N VAL B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 177 " --> pdb=" O HIS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 removed outlier: 3.873A pdb=" N SER B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.897A pdb=" N ARG B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 372 through 384 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.947A pdb=" N LEU B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 Processing helix chain 'B' and resid 422 through 435 removed outlier: 4.441A pdb=" N MET B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 4.009A pdb=" N VAL B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.572A pdb=" N PHE B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.572A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.628A pdb=" N TRP B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 581 removed outlier: 4.084A pdb=" N TYR B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 600 removed outlier: 3.900A pdb=" N SER B 588 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 590 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 632 removed outlier: 4.197A pdb=" N ASP B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.651A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 650 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.887A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 removed outlier: 4.044A pdb=" N GLN B 673 " --> pdb=" O GLN B 669 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.753A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 703 removed outlier: 3.515A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 767 through 776 removed outlier: 3.885A pdb=" N PHE B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B 776 " --> pdb=" O TRP B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 803 removed outlier: 3.559A pdb=" N ILE B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET B 784 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 835 removed outlier: 4.478A pdb=" N LEU B 817 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 835 " --> pdb=" O GLN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.975A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 860 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 removed outlier: 3.506A pdb=" N GLN B 866 " --> pdb=" O ASP B 862 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 883 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.913A pdb=" N GLY B 891 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG B 892 " --> pdb=" O TYR B 888 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 897 " --> pdb=" O THR B 893 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 removed outlier: 4.517A pdb=" N ILE B 909 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 911 " --> pdb=" O HIS B 908 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 912 " --> pdb=" O ILE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 925 removed outlier: 3.849A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE B 922 " --> pdb=" O PRO B 918 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 953 removed outlier: 4.024A pdb=" N ALA B 943 " --> pdb=" O VAL B 939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 944 " --> pdb=" O TRP B 940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG B 953 " --> pdb=" O GLU B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 removed outlier: 3.871A pdb=" N ILE B 962 " --> pdb=" O ASP B 958 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix Processing helix chain 'B' and resid 1017 through 1034 removed outlier: 3.798A pdb=" N VAL B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1061 removed outlier: 3.733A pdb=" N LYS B1049 " --> pdb=" O TYR B1045 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B1061 " --> pdb=" O TYR B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1072 removed outlier: 4.056A pdb=" N PHE B1069 " --> pdb=" O LEU B1065 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B1070 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B1072 " --> pdb=" O GLU B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1088 Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 3.666A pdb=" N THR B1123 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B1128 " --> pdb=" O TRP B1124 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B1134 " --> pdb=" O GLU B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1163 Processing helix chain 'B' and resid 1165 through 1192 removed outlier: 4.146A pdb=" N GLU B1169 " --> pdb=" O ILE B1165 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B1170 " --> pdb=" O ARG B1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 109 removed outlier: 4.137A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.551A pdb=" N GLN C 135 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 removed outlier: 3.689A pdb=" N VAL C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 177 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.873A pdb=" N SER C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 removed outlier: 3.896A pdb=" N ARG C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 372 through 384 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.948A pdb=" N LEU C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 415 Processing helix chain 'C' and resid 422 through 435 removed outlier: 4.440A pdb=" N MET C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 4.008A pdb=" N VAL C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 442 " --> pdb=" O PRO C 438 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.571A pdb=" N PHE C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.571A pdb=" N LEU C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.627A pdb=" N TRP C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 569 " --> pdb=" O TRP C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 4.084A pdb=" N TYR C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 600 removed outlier: 3.900A pdb=" N SER C 588 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 632 removed outlier: 4.197A pdb=" N ASP C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.651A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 644 " --> pdb=" O ARG C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 650 Processing helix chain 'C' and resid 654 through 660 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.887A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 removed outlier: 4.043A pdb=" N GLN C 673 " --> pdb=" O GLN C 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN C 678 " --> pdb=" O SER C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.755A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 703 removed outlier: 3.515A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 767 through 776 removed outlier: 3.885A pdb=" N PHE C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP C 776 " --> pdb=" O TRP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 803 removed outlier: 3.559A pdb=" N ILE C 782 " --> pdb=" O ALA C 778 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET C 784 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 835 removed outlier: 4.478A pdb=" N LEU C 817 " --> pdb=" O LEU C 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.974A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 860 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.507A pdb=" N GLN C 866 " --> pdb=" O ASP C 862 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 883 " --> pdb=" O VAL C 879 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.914A pdb=" N GLY C 891 " --> pdb=" O LEU C 887 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 892 " --> pdb=" O TYR C 888 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 897 " --> pdb=" O THR C 893 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.518A pdb=" N ILE C 909 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 911 " --> pdb=" O HIS C 908 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 912 " --> pdb=" O ILE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 925 removed outlier: 3.849A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 922 " --> pdb=" O PRO C 918 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 953 removed outlier: 4.024A pdb=" N ALA C 943 " --> pdb=" O VAL C 939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 944 " --> pdb=" O TRP C 940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 953 " --> pdb=" O GLU C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 972 removed outlier: 3.871A pdb=" N ILE C 962 " --> pdb=" O ASP C 958 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix Processing helix chain 'C' and resid 1017 through 1034 removed outlier: 3.799A pdb=" N VAL C1021 " --> pdb=" O ASN C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1061 removed outlier: 3.734A pdb=" N LYS C1049 " --> pdb=" O TYR C1045 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C1056 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C1061 " --> pdb=" O TYR C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1072 removed outlier: 4.056A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C1070 " --> pdb=" O ILE C1066 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C1072 " --> pdb=" O GLU C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1088 Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 3.667A pdb=" N THR C1123 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS C1128 " --> pdb=" O TRP C1124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C1134 " --> pdb=" O GLU C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1163 Processing helix chain 'C' and resid 1165 through 1192 removed outlier: 4.146A pdb=" N GLU C1169 " --> pdb=" O ILE C1165 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C1170 " --> pdb=" O ARG C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 109 removed outlier: 4.137A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.551A pdb=" N GLN D 135 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 177 removed outlier: 3.689A pdb=" N VAL D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 removed outlier: 3.873A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 removed outlier: 3.897A pdb=" N ARG D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 328 through 333 Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 372 through 384 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.948A pdb=" N LEU D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 415 Processing helix chain 'D' and resid 422 through 435 removed outlier: 4.439A pdb=" N MET D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 removed outlier: 4.009A pdb=" N VAL D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG D 442 " --> pdb=" O PRO D 438 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 455 removed outlier: 3.572A pdb=" N PHE D 454 " --> pdb=" O SER D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.572A pdb=" N LEU D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.627A pdb=" N TRP D 565 " --> pdb=" O ASP D 561 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 569 " --> pdb=" O TRP D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 removed outlier: 4.085A pdb=" N TYR D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 600 removed outlier: 3.900A pdb=" N SER D 588 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 590 " --> pdb=" O VAL D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 632 removed outlier: 4.196A pdb=" N ASP D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.650A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 650 Processing helix chain 'D' and resid 654 through 660 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.888A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 removed outlier: 4.043A pdb=" N GLN D 673 " --> pdb=" O GLN D 669 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.755A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 703 removed outlier: 3.516A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 767 through 776 removed outlier: 3.885A pdb=" N PHE D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP D 776 " --> pdb=" O TRP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 803 removed outlier: 3.559A pdb=" N ILE D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET D 784 " --> pdb=" O VAL D 780 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 835 removed outlier: 4.478A pdb=" N LEU D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY D 835 " --> pdb=" O GLN D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 860 removed outlier: 3.975A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 860 " --> pdb=" O LEU D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 removed outlier: 3.506A pdb=" N GLN D 866 " --> pdb=" O ASP D 862 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 883 " --> pdb=" O VAL D 879 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.913A pdb=" N GLY D 891 " --> pdb=" O LEU D 887 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D 892 " --> pdb=" O TYR D 888 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 897 " --> pdb=" O THR D 893 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 901 " --> pdb=" O ILE D 897 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 removed outlier: 4.517A pdb=" N ILE D 909 " --> pdb=" O LEU D 906 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR D 911 " --> pdb=" O HIS D 908 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 912 " --> pdb=" O ILE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 925 removed outlier: 3.850A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE D 922 " --> pdb=" O PRO D 918 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL D 923 " --> pdb=" O LYS D 919 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 953 removed outlier: 4.025A pdb=" N ALA D 943 " --> pdb=" O VAL D 939 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 944 " --> pdb=" O TRP D 940 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 953 " --> pdb=" O GLU D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 972 removed outlier: 3.871A pdb=" N ILE D 962 " --> pdb=" O ASP D 958 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix Processing helix chain 'D' and resid 1017 through 1034 removed outlier: 3.799A pdb=" N VAL D1021 " --> pdb=" O ASN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1061 removed outlier: 3.734A pdb=" N LYS D1049 " --> pdb=" O TYR D1045 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D1056 " --> pdb=" O GLY D1052 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D1061 " --> pdb=" O TYR D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1072 removed outlier: 4.057A pdb=" N PHE D1069 " --> pdb=" O LEU D1065 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS D1070 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D1072 " --> pdb=" O GLU D1068 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1088 Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 3.666A pdb=" N THR D1123 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS D1128 " --> pdb=" O TRP D1124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D1134 " --> pdb=" O GLU D1130 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1163 Processing helix chain 'D' and resid 1165 through 1192 removed outlier: 4.146A pdb=" N GLU D1169 " --> pdb=" O ILE D1165 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN D1170 " --> pdb=" O ARG D1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 3.650A pdb=" N GLY A 76 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET A 186 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 117 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 154 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLY A 156 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N VAL A 121 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS A 298 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 646 removed outlier: 4.656A pdb=" N ALA A 652 " --> pdb=" O CYS A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1000 through 1001 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78 removed outlier: 3.650A pdb=" N GLY B 76 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET B 186 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 117 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 154 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 119 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLY B 156 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N VAL B 121 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS B 298 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 645 through 646 removed outlier: 4.656A pdb=" N ALA B 652 " --> pdb=" O CYS B 646 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1000 through 1001 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 78 removed outlier: 3.650A pdb=" N GLY C 76 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N MET C 186 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 117 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 154 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLY C 156 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N VAL C 121 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 298 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 645 through 646 removed outlier: 4.655A pdb=" N ALA C 652 " --> pdb=" O CYS C 646 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1000 through 1001 Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 17 Processing sheet with id=AB5, first strand: chain 'D' and resid 75 through 78 removed outlier: 3.650A pdb=" N GLY D 76 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N MET D 186 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 117 " --> pdb=" O TRP D 152 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL D 154 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 119 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N GLY D 156 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N VAL D 121 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS D 298 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 645 through 646 removed outlier: 4.655A pdb=" N ALA D 652 " --> pdb=" O CYS D 646 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1000 through 1001 1440 hydrogen bonds defined for protein. 4260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.89: 29580 1.89 - 2.57: 256 2.57 - 3.25: 0 3.25 - 3.92: 16 3.92 - 4.60: 16 Bond restraints: 29868 Sorted by residual: bond pdb=" O16 DVT B2002 " pdb=" V8 DVT B2002 " ideal model delta sigma weight residual 2.084 4.400 -2.316 2.00e-02 2.50e+03 1.34e+04 bond pdb=" O16 DVT C2001 " pdb=" V8 DVT C2001 " ideal model delta sigma weight residual 2.084 4.400 -2.316 2.00e-02 2.50e+03 1.34e+04 bond pdb=" O16 DVT B2001 " pdb=" V8 DVT B2001 " ideal model delta sigma weight residual 2.084 4.400 -2.316 2.00e-02 2.50e+03 1.34e+04 bond pdb=" O16 DVT A2001 " pdb=" V8 DVT A2001 " ideal model delta sigma weight residual 2.084 4.399 -2.315 2.00e-02 2.50e+03 1.34e+04 bond pdb=" O16 DVT D2002 " pdb=" V8 DVT D2002 " ideal model delta sigma weight residual 2.084 4.399 -2.315 2.00e-02 2.50e+03 1.34e+04 ... (remaining 29863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.48: 41424 20.48 - 40.96: 120 40.96 - 61.44: 80 61.44 - 81.92: 56 81.92 - 102.40: 40 Bond angle restraints: 41720 Sorted by residual: angle pdb=" V2 DVT A2002 " pdb=" O16 DVT A2002 " pdb=" V6 DVT A2002 " ideal model delta sigma weight residual 174.97 72.57 102.40 3.00e+00 1.11e-01 1.17e+03 angle pdb=" V2 DVT B2002 " pdb=" O16 DVT B2002 " pdb=" V6 DVT B2002 " ideal model delta sigma weight residual 174.97 72.57 102.40 3.00e+00 1.11e-01 1.17e+03 angle pdb=" V2 DVT C2002 " pdb=" O16 DVT C2002 " pdb=" V6 DVT C2002 " ideal model delta sigma weight residual 174.97 72.57 102.40 3.00e+00 1.11e-01 1.17e+03 angle pdb=" V2 DVT B2001 " pdb=" O16 DVT B2001 " pdb=" V6 DVT B2001 " ideal model delta sigma weight residual 174.97 72.58 102.39 3.00e+00 1.11e-01 1.16e+03 angle pdb=" V2 DVT C2001 " pdb=" O16 DVT C2001 " pdb=" V6 DVT C2001 " ideal model delta sigma weight residual 174.97 72.58 102.39 3.00e+00 1.11e-01 1.16e+03 ... (remaining 41715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 16532 18.33 - 36.65: 586 36.65 - 54.98: 78 54.98 - 73.30: 44 73.30 - 91.63: 8 Dihedral angle restraints: 17248 sinusoidal: 6056 harmonic: 11192 Sorted by residual: dihedral pdb=" CA LEU D 277 " pdb=" C LEU D 277 " pdb=" N ILE D 278 " pdb=" CA ILE D 278 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU C 277 " pdb=" C LEU C 277 " pdb=" N ILE C 278 " pdb=" CA ILE C 278 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU A 277 " pdb=" C LEU A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 17245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3959 0.075 - 0.150: 629 0.150 - 0.225: 68 0.225 - 0.300: 12 0.300 - 0.375: 4 Chirality restraints: 4672 Sorted by residual: chirality pdb=" CA ASN B1032 " pdb=" N ASN B1032 " pdb=" C ASN B1032 " pdb=" CB ASN B1032 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA ASN D1032 " pdb=" N ASN D1032 " pdb=" C ASN D1032 " pdb=" CB ASN D1032 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA ASN A1032 " pdb=" N ASN A1032 " pdb=" C ASN A1032 " pdb=" CB ASN A1032 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4669 not shown) Planarity restraints: 5068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 83 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ALA B 83 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA B 83 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 84 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 83 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ALA C 83 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA C 83 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY C 84 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 83 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ALA A 83 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA A 83 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY A 84 " -0.020 2.00e-02 2.50e+03 ... (remaining 5065 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 256 2.65 - 3.21: 25273 3.21 - 3.77: 41390 3.77 - 4.34: 49383 4.34 - 4.90: 84641 Nonbonded interactions: 200943 Sorted by model distance: nonbonded pdb=" O7 DVT C2002 " pdb=" V8 DVT C2002 " model vdw 2.083 2.440 nonbonded pdb=" O7 DVT A2002 " pdb=" V8 DVT A2002 " model vdw 2.083 2.440 nonbonded pdb=" O7 DVT B2002 " pdb=" V8 DVT B2002 " model vdw 2.083 2.440 nonbonded pdb=" O7 DVT D2002 " pdb=" V8 DVT D2002 " model vdw 2.083 2.440 nonbonded pdb=" O7 DVT D2001 " pdb=" V8 DVT D2001 " model vdw 2.085 2.440 ... (remaining 200938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.980 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.062 2.316 29868 Z= 3.073 Angle : 4.808 102.405 41720 Z= 1.670 Chirality : 0.058 0.375 4672 Planarity : 0.009 0.108 5068 Dihedral : 10.881 91.628 10024 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.30 % Allowed : 4.45 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.11), residues: 3836 helix: -1.67 (0.09), residues: 2232 sheet: -2.87 (0.24), residues: 256 loop : -3.38 (0.13), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 287 TYR 0.027 0.003 TYR B 818 PHE 0.026 0.003 PHE D1043 TRP 0.029 0.003 TRP D 10 HIS 0.008 0.002 HIS C 774 Details of bonding type rmsd covalent geometry : bond 0.06160 (29868) covalent geometry : angle 4.80751 (41720) hydrogen bonds : bond 0.13284 ( 1440) hydrogen bonds : angle 5.38941 ( 4260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 LEU cc_start: 0.8985 (mt) cc_final: 0.8671 (tt) REVERT: B 675 LEU cc_start: 0.8998 (mt) cc_final: 0.8694 (tt) REVERT: C 675 LEU cc_start: 0.8999 (mt) cc_final: 0.8692 (tt) REVERT: D 675 LEU cc_start: 0.9003 (mt) cc_final: 0.8686 (tt) outliers start: 8 outliers final: 0 residues processed: 188 average time/residue: 0.2122 time to fit residues: 63.5172 Evaluate side-chains 104 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN B1014 GLN ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 GLN C1014 GLN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.079925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061741 restraints weight = 103329.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.062779 restraints weight = 64732.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063009 restraints weight = 48958.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063340 restraints weight = 49171.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063444 restraints weight = 43767.390| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29868 Z= 0.127 Angle : 0.567 8.162 41720 Z= 0.290 Chirality : 0.037 0.116 4672 Planarity : 0.005 0.050 5068 Dihedral : 4.872 21.480 4332 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.60 % Allowed : 6.04 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3836 helix: 0.26 (0.11), residues: 2236 sheet: -2.57 (0.25), residues: 256 loop : -3.13 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1141 TYR 0.014 0.001 TYR B 577 PHE 0.011 0.001 PHE C 373 TRP 0.017 0.001 TRP C1058 HIS 0.004 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00270 (29868) covalent geometry : angle 0.56698 (41720) hydrogen bonds : bond 0.05288 ( 1440) hydrogen bonds : angle 4.03211 ( 4260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.8504 (tpp) cc_final: 0.8231 (mpp) REVERT: B 581 MET cc_start: 0.8560 (tpp) cc_final: 0.8270 (mpp) REVERT: C 581 MET cc_start: 0.8554 (tpp) cc_final: 0.8263 (mpp) REVERT: D 581 MET cc_start: 0.8552 (tpp) cc_final: 0.8266 (mpp) outliers start: 42 outliers final: 26 residues processed: 159 average time/residue: 0.1670 time to fit residues: 46.2047 Evaluate side-chains 129 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 939 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 368 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 361 optimal weight: 2.9990 chunk 115 optimal weight: 0.0170 chunk 127 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 307 optimal weight: 0.0020 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064479 restraints weight = 107866.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065087 restraints weight = 75116.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065483 restraints weight = 57547.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.065965 restraints weight = 53787.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066113 restraints weight = 47913.012| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29868 Z= 0.091 Angle : 0.481 10.065 41720 Z= 0.244 Chirality : 0.034 0.117 4672 Planarity : 0.004 0.045 5068 Dihedral : 4.113 18.140 4332 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.41 % Allowed : 7.67 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.64 (0.14), residues: 3836 helix: 1.14 (0.11), residues: 2252 sheet: -2.25 (0.25), residues: 264 loop : -2.91 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 965 TYR 0.008 0.001 TYR D 818 PHE 0.011 0.001 PHE A 899 TRP 0.014 0.001 TRP A1058 HIS 0.003 0.000 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00188 (29868) covalent geometry : angle 0.48060 (41720) hydrogen bonds : bond 0.03490 ( 1440) hydrogen bonds : angle 3.46916 ( 4260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.8461 (tpp) cc_final: 0.8084 (mpp) REVERT: B 581 MET cc_start: 0.8478 (tpp) cc_final: 0.8117 (mpp) REVERT: C 581 MET cc_start: 0.8471 (tpp) cc_final: 0.8109 (mpp) REVERT: D 581 MET cc_start: 0.8479 (tpp) cc_final: 0.8123 (mpp) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.1783 time to fit residues: 51.5678 Evaluate side-chains 137 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 258 optimal weight: 3.9990 chunk 338 optimal weight: 0.2980 chunk 152 optimal weight: 0.0470 chunk 322 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063337 restraints weight = 105122.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064256 restraints weight = 66682.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064548 restraints weight = 50695.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064764 restraints weight = 51000.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065018 restraints weight = 45681.396| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 29868 Z= 0.088 Angle : 0.452 8.130 41720 Z= 0.231 Chirality : 0.034 0.118 4672 Planarity : 0.004 0.047 5068 Dihedral : 3.820 17.249 4332 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.63 % Allowed : 7.52 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3836 helix: 1.68 (0.12), residues: 2236 sheet: -2.09 (0.26), residues: 264 loop : -2.78 (0.14), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 357 TYR 0.007 0.001 TYR B1057 PHE 0.008 0.001 PHE B 805 TRP 0.011 0.001 TRP A1058 HIS 0.002 0.000 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00195 (29868) covalent geometry : angle 0.45226 (41720) hydrogen bonds : bond 0.03345 ( 1440) hydrogen bonds : angle 3.32454 ( 4260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.241 Fit side-chains REVERT: A 581 MET cc_start: 0.8445 (tpp) cc_final: 0.8138 (tpp) REVERT: A 1042 MET cc_start: 0.8233 (tpp) cc_final: 0.8026 (mtp) REVERT: B 581 MET cc_start: 0.8484 (tpp) cc_final: 0.8160 (tpp) REVERT: C 581 MET cc_start: 0.8470 (tpp) cc_final: 0.8150 (tpp) REVERT: D 581 MET cc_start: 0.8473 (tpp) cc_final: 0.8153 (tpp) outliers start: 43 outliers final: 26 residues processed: 159 average time/residue: 0.1627 time to fit residues: 44.8930 Evaluate side-chains 131 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 85 optimal weight: 2.9990 chunk 142 optimal weight: 0.0170 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 152 optimal weight: 0.1980 chunk 280 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061935 restraints weight = 108688.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062425 restraints weight = 78081.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.062711 restraints weight = 60589.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063160 restraints weight = 56522.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.063392 restraints weight = 51354.710| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29868 Z= 0.145 Angle : 0.510 9.168 41720 Z= 0.254 Chirality : 0.036 0.113 4672 Planarity : 0.004 0.046 5068 Dihedral : 3.791 17.767 4332 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.29 % Allowed : 8.47 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3836 helix: 2.02 (0.12), residues: 2240 sheet: -1.89 (0.27), residues: 264 loop : -2.71 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 353 TYR 0.009 0.001 TYR B 464 PHE 0.009 0.001 PHE D 783 TRP 0.010 0.001 TRP A1058 HIS 0.003 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00336 (29868) covalent geometry : angle 0.51018 (41720) hydrogen bonds : bond 0.04022 ( 1440) hydrogen bonds : angle 3.47587 ( 4260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.328 Fit side-chains outliers start: 34 outliers final: 32 residues processed: 134 average time/residue: 0.1507 time to fit residues: 37.0858 Evaluate side-chains 132 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 357 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058877 restraints weight = 109039.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059226 restraints weight = 81650.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059654 restraints weight = 61017.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.060079 restraints weight = 58482.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060212 restraints weight = 51737.884| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29868 Z= 0.233 Angle : 0.614 7.549 41720 Z= 0.309 Chirality : 0.040 0.115 4672 Planarity : 0.005 0.048 5068 Dihedral : 4.195 20.385 4332 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.94 % Allowed : 8.70 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3836 helix: 1.96 (0.12), residues: 2240 sheet: -1.92 (0.27), residues: 260 loop : -2.71 (0.15), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.012 0.002 TYR B1057 PHE 0.017 0.002 PHE D1043 TRP 0.014 0.002 TRP D 10 HIS 0.005 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00539 (29868) covalent geometry : angle 0.61423 (41720) hydrogen bonds : bond 0.05725 ( 1440) hydrogen bonds : angle 3.95159 ( 4260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 1.073 Fit side-chains outliers start: 51 outliers final: 47 residues processed: 139 average time/residue: 0.1460 time to fit residues: 37.3583 Evaluate side-chains 135 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 88 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 896 CYS Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 1050 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 896 CYS Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 896 CYS Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 939 VAL Chi-restraints excluded: chain D residue 1050 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 251 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 372 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 333 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 307 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060993 restraints weight = 105427.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061840 restraints weight = 67969.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062182 restraints weight = 51785.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062386 restraints weight = 52448.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062665 restraints weight = 46740.615| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 29868 Z= 0.109 Angle : 0.486 7.950 41720 Z= 0.245 Chirality : 0.035 0.114 4672 Planarity : 0.004 0.044 5068 Dihedral : 3.876 18.945 4332 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.14 % Allowed : 9.65 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3836 helix: 2.19 (0.12), residues: 2248 sheet: -1.78 (0.27), residues: 260 loop : -2.61 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 459 TYR 0.009 0.001 TYR A1057 PHE 0.010 0.001 PHE A 805 TRP 0.014 0.001 TRP A1058 HIS 0.004 0.000 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00245 (29868) covalent geometry : angle 0.48606 (41720) hydrogen bonds : bond 0.04117 ( 1440) hydrogen bonds : angle 3.49886 ( 4260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.106 Fit side-chains REVERT: A 1042 MET cc_start: 0.8325 (tpp) cc_final: 0.8008 (mtp) outliers start: 30 outliers final: 30 residues processed: 131 average time/residue: 0.1509 time to fit residues: 35.9905 Evaluate side-chains 133 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 820 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 820 TRP Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 820 TRP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 820 TRP Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 87 optimal weight: 0.0980 chunk 113 optimal weight: 0.0370 chunk 51 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 116 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 373 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 overall best weight: 0.3868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B1017 ASN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062708 restraints weight = 102858.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063558 restraints weight = 65082.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063926 restraints weight = 49468.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.064131 restraints weight = 49667.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064377 restraints weight = 44457.194| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29868 Z= 0.085 Angle : 0.455 6.845 41720 Z= 0.229 Chirality : 0.034 0.121 4672 Planarity : 0.004 0.042 5068 Dihedral : 3.619 17.620 4332 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.33 % Allowed : 9.42 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3836 helix: 2.40 (0.12), residues: 2244 sheet: -1.66 (0.27), residues: 260 loop : -2.52 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.007 0.001 TYR C1057 PHE 0.009 0.001 PHE C 805 TRP 0.013 0.001 TRP A1058 HIS 0.003 0.000 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00185 (29868) covalent geometry : angle 0.45464 (41720) hydrogen bonds : bond 0.03155 ( 1440) hydrogen bonds : angle 3.18822 ( 4260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.263 Fit side-chains REVERT: A 186 MET cc_start: 0.7128 (ptt) cc_final: 0.6891 (ptm) REVERT: C 186 MET cc_start: 0.7135 (ptt) cc_final: 0.6904 (ptm) outliers start: 35 outliers final: 26 residues processed: 140 average time/residue: 0.1516 time to fit residues: 38.6991 Evaluate side-chains 130 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 820 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 820 TRP Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 820 TRP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 820 TRP Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 248 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 281 optimal weight: 0.0000 chunk 173 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060795 restraints weight = 103310.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.061824 restraints weight = 66732.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061985 restraints weight = 49914.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062213 restraints weight = 52189.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062450 restraints weight = 46264.321| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29868 Z= 0.134 Angle : 0.498 7.027 41720 Z= 0.248 Chirality : 0.036 0.114 4672 Planarity : 0.004 0.044 5068 Dihedral : 3.657 18.268 4332 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.25 % Allowed : 9.57 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3836 helix: 2.38 (0.12), residues: 2244 sheet: -1.73 (0.26), residues: 264 loop : -2.44 (0.15), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.009 0.001 TYR B1063 PHE 0.010 0.001 PHE B 805 TRP 0.010 0.001 TRP A1058 HIS 0.004 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00312 (29868) covalent geometry : angle 0.49793 (41720) hydrogen bonds : bond 0.03928 ( 1440) hydrogen bonds : angle 3.38846 ( 4260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.133 Fit side-chains REVERT: A 186 MET cc_start: 0.7397 (ptp) cc_final: 0.7099 (ptm) REVERT: B 430 MET cc_start: 0.9055 (tpp) cc_final: 0.8582 (mmm) REVERT: C 186 MET cc_start: 0.7398 (ptp) cc_final: 0.7105 (ptm) REVERT: C 926 MET cc_start: 0.8725 (mmm) cc_final: 0.8459 (mmm) REVERT: D 430 MET cc_start: 0.9059 (tpp) cc_final: 0.8589 (mmm) outliers start: 33 outliers final: 31 residues processed: 136 average time/residue: 0.1458 time to fit residues: 36.0637 Evaluate side-chains 130 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 820 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 820 TRP Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 820 TRP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 820 TRP Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 153 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 342 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 367 optimal weight: 0.9990 chunk 145 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.062300 restraints weight = 104748.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063102 restraints weight = 68087.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063793 restraints weight = 51837.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063979 restraints weight = 49126.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064096 restraints weight = 44350.723| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 29868 Z= 0.087 Angle : 0.450 7.396 41720 Z= 0.225 Chirality : 0.034 0.119 4672 Planarity : 0.004 0.042 5068 Dihedral : 3.539 17.396 4332 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.95 % Allowed : 9.95 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3836 helix: 2.47 (0.12), residues: 2244 sheet: -1.95 (0.27), residues: 220 loop : -2.32 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.007 0.001 TYR A1057 PHE 0.009 0.001 PHE A 805 TRP 0.013 0.001 TRP A1058 HIS 0.009 0.001 HIS D1002 Details of bonding type rmsd covalent geometry : bond 0.00193 (29868) covalent geometry : angle 0.45047 (41720) hydrogen bonds : bond 0.03199 ( 1440) hydrogen bonds : angle 3.16665 ( 4260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.200 Fit side-chains REVERT: A 186 MET cc_start: 0.7180 (ptp) cc_final: 0.6941 (ptm) REVERT: A 430 MET cc_start: 0.9111 (mmm) cc_final: 0.8862 (tpp) REVERT: B 430 MET cc_start: 0.8980 (tpp) cc_final: 0.8545 (mmm) REVERT: B 988 MET cc_start: 0.8530 (mmm) cc_final: 0.8103 (mmt) REVERT: C 186 MET cc_start: 0.7192 (ptp) cc_final: 0.6952 (ptm) REVERT: C 430 MET cc_start: 0.9102 (mmm) cc_final: 0.8854 (tpp) REVERT: C 926 MET cc_start: 0.8692 (mmm) cc_final: 0.8459 (mmm) REVERT: D 430 MET cc_start: 0.8989 (tpp) cc_final: 0.8554 (mmm) outliers start: 25 outliers final: 23 residues processed: 125 average time/residue: 0.1530 time to fit residues: 34.8249 Evaluate side-chains 123 residues out of total 3288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 820 TRP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 820 TRP Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 820 TRP Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 820 TRP Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 937 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 80 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060494 restraints weight = 109124.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060915 restraints weight = 78699.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.061420 restraints weight = 61565.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061719 restraints weight = 57168.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.061828 restraints weight = 50490.656| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29868 Z= 0.178 Angle : 0.537 7.066 41720 Z= 0.266 Chirality : 0.037 0.111 4672 Planarity : 0.004 0.045 5068 Dihedral : 3.753 18.841 4332 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.22 % Allowed : 9.88 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3836 helix: 2.39 (0.12), residues: 2244 sheet: -1.61 (0.26), residues: 264 loop : -2.36 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 965 TYR 0.010 0.001 TYR A1063 PHE 0.014 0.001 PHE A 783 TRP 0.012 0.001 TRP A 691 HIS 0.008 0.001 HIS D1002 Details of bonding type rmsd covalent geometry : bond 0.00411 (29868) covalent geometry : angle 0.53707 (41720) hydrogen bonds : bond 0.04579 ( 1440) hydrogen bonds : angle 3.52824 ( 4260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3802.87 seconds wall clock time: 66 minutes 27.93 seconds (3987.93 seconds total)