Starting phenix.real_space_refine on Sun Dec 29 23:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8l_16483/12_2024/8c8l_16483.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 36330 2.51 5 N 9570 2.21 5 O 13068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 546 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59076 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Chain: "B" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Chain: "C" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Chain: "E" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Chain: "F" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 9846 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 4, 'PTRANS': 39, 'TRANS': 1283} Time building chain proxies: 24.81, per 1000 atoms: 0.42 Number of scatterers: 59076 At special positions: 0 Unit cell: (241.332, 245.7, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 13068 8.00 N 9570 7.00 C 36330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 345 " distance=2.05 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 962 " distance=2.04 Simple disulfide: pdb=" SG CYS A1166 " - pdb=" SG CYS A1199 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 177 " distance=2.05 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 345 " distance=2.04 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 962 " distance=2.03 Simple disulfide: pdb=" SG CYS B1166 " - pdb=" SG CYS B1199 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 177 " distance=2.06 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 345 " distance=2.06 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 962 " distance=2.03 Simple disulfide: pdb=" SG CYS C1166 " - pdb=" SG CYS C1199 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 341 " - pdb=" SG CYS D 345 " distance=2.05 Simple disulfide: pdb=" SG CYS D 920 " - pdb=" SG CYS D 962 " distance=2.04 Simple disulfide: pdb=" SG CYS D1166 " - pdb=" SG CYS D1199 " distance=2.02 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 177 " distance=2.05 Simple disulfide: pdb=" SG CYS E 341 " - pdb=" SG CYS E 345 " distance=2.04 Simple disulfide: pdb=" SG CYS E 920 " - pdb=" SG CYS E 962 " distance=2.03 Simple disulfide: pdb=" SG CYS E1166 " - pdb=" SG CYS E1199 " distance=2.02 Simple disulfide: pdb=" SG CYS F 128 " - pdb=" SG CYS F 177 " distance=2.06 Simple disulfide: pdb=" SG CYS F 341 " - pdb=" SG CYS F 345 " distance=2.06 Simple disulfide: pdb=" SG CYS F 920 " - pdb=" SG CYS F 962 " distance=2.03 Simple disulfide: pdb=" SG CYS F1166 " - pdb=" SG CYS F1199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.24 Conformation dependent library (CDL) restraints added in 6.3 seconds 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14556 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 138 sheets defined 12.8% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.71 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.797A pdb=" N LEU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.546A pdb=" N ALA A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 481 through 484 Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.664A pdb=" N THR A 564 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.672A pdb=" N GLU A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 Processing helix chain 'A' and resid 681 through 689 removed outlier: 3.827A pdb=" N SER A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 769 through 772 Processing helix chain 'A' and resid 773 through 779 removed outlier: 4.415A pdb=" N PHE A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 850 through 853 Processing helix chain 'A' and resid 919 through 926 Processing helix chain 'A' and resid 933 through 937 removed outlier: 3.515A pdb=" N THR A 937 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1050 through 1054 Processing helix chain 'A' and resid 1059 through 1063 removed outlier: 4.084A pdb=" N GLU A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 4.281A pdb=" N SER A1168 " --> pdb=" O GLN A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.782A pdb=" N ARG A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1259 removed outlier: 3.604A pdb=" N ASP A1259 " --> pdb=" O PRO A1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1256 through 1259' Processing helix chain 'A' and resid 1269 through 1271 No H-bonds generated for 'chain 'A' and resid 1269 through 1271' Processing helix chain 'A' and resid 1291 through 1297 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.799A pdb=" N LEU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.554A pdb=" N ALA B 263 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 481 through 484 Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.665A pdb=" N THR B 564 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.673A pdb=" N GLU B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 633 Processing helix chain 'B' and resid 681 through 689 removed outlier: 3.830A pdb=" N SER B 685 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 735 No H-bonds generated for 'chain 'B' and resid 733 through 735' Processing helix chain 'B' and resid 769 through 772 Processing helix chain 'B' and resid 773 through 779 removed outlier: 4.388A pdb=" N PHE B 777 " --> pdb=" O ASP B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 850 through 853 Processing helix chain 'B' and resid 919 through 926 Processing helix chain 'B' and resid 933 through 937 removed outlier: 3.515A pdb=" N THR B 937 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1059 through 1063 removed outlier: 4.084A pdb=" N GLU B1063 " --> pdb=" O SER B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1164 through 1169 removed outlier: 4.286A pdb=" N SER B1168 " --> pdb=" O GLN B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1183 through 1188 removed outlier: 3.779A pdb=" N ARG B1187 " --> pdb=" O ALA B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1259 removed outlier: 3.608A pdb=" N ASP B1259 " --> pdb=" O PRO B1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1256 through 1259' Processing helix chain 'B' and resid 1269 through 1271 No H-bonds generated for 'chain 'B' and resid 1269 through 1271' Processing helix chain 'B' and resid 1291 through 1297 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 178 through 185 removed outlier: 3.795A pdb=" N LEU C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.544A pdb=" N ALA C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 481 through 484 Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 560 through 564 removed outlier: 3.663A pdb=" N THR C 564 " --> pdb=" O SER C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 610 removed outlier: 3.670A pdb=" N GLU C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 633 Processing helix chain 'C' and resid 681 through 689 removed outlier: 3.826A pdb=" N SER C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 735 No H-bonds generated for 'chain 'C' and resid 733 through 735' Processing helix chain 'C' and resid 769 through 772 Processing helix chain 'C' and resid 773 through 779 removed outlier: 4.419A pdb=" N PHE C 777 " --> pdb=" O ASP C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 919 through 926 Processing helix chain 'C' and resid 933 through 937 removed outlier: 3.515A pdb=" N THR C 937 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1033 Processing helix chain 'C' and resid 1050 through 1054 Processing helix chain 'C' and resid 1059 through 1063 removed outlier: 4.086A pdb=" N GLU C1063 " --> pdb=" O SER C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1081 Processing helix chain 'C' and resid 1129 through 1133 Processing helix chain 'C' and resid 1164 through 1169 removed outlier: 4.284A pdb=" N SER C1168 " --> pdb=" O GLN C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1188 removed outlier: 3.777A pdb=" N ARG C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1256 through 1259 removed outlier: 3.606A pdb=" N ASP C1259 " --> pdb=" O PRO C1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1256 through 1259' Processing helix chain 'C' and resid 1269 through 1271 No H-bonds generated for 'chain 'C' and resid 1269 through 1271' Processing helix chain 'C' and resid 1291 through 1297 Processing helix chain 'D' and resid 105 through 113 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 178 through 185 removed outlier: 3.798A pdb=" N LEU D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.545A pdb=" N ALA D 263 " --> pdb=" O ASP D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 393 through 398 Processing helix chain 'D' and resid 481 through 484 Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.667A pdb=" N THR D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 610 removed outlier: 3.673A pdb=" N GLU D 610 " --> pdb=" O GLU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 633 Processing helix chain 'D' and resid 681 through 689 removed outlier: 3.825A pdb=" N SER D 685 " --> pdb=" O THR D 681 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 735 No H-bonds generated for 'chain 'D' and resid 733 through 735' Processing helix chain 'D' and resid 769 through 772 Processing helix chain 'D' and resid 773 through 779 removed outlier: 4.415A pdb=" N PHE D 777 " --> pdb=" O ASP D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 800 Processing helix chain 'D' and resid 850 through 853 Processing helix chain 'D' and resid 919 through 926 Processing helix chain 'D' and resid 933 through 937 removed outlier: 3.515A pdb=" N THR D 937 " --> pdb=" O LEU D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1033 Processing helix chain 'D' and resid 1050 through 1054 Processing helix chain 'D' and resid 1059 through 1063 removed outlier: 4.085A pdb=" N GLU D1063 " --> pdb=" O SER D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1081 Processing helix chain 'D' and resid 1129 through 1133 Processing helix chain 'D' and resid 1164 through 1169 removed outlier: 4.280A pdb=" N SER D1168 " --> pdb=" O GLN D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1188 removed outlier: 3.781A pdb=" N ARG D1187 " --> pdb=" O ALA D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1256 through 1259 removed outlier: 3.607A pdb=" N ASP D1259 " --> pdb=" O PRO D1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1256 through 1259' Processing helix chain 'D' and resid 1269 through 1271 No H-bonds generated for 'chain 'D' and resid 1269 through 1271' Processing helix chain 'D' and resid 1291 through 1297 Processing helix chain 'E' and resid 105 through 113 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 178 through 185 removed outlier: 3.799A pdb=" N LEU E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.555A pdb=" N ALA E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 288 Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 393 through 398 Processing helix chain 'E' and resid 481 through 484 Processing helix chain 'E' and resid 533 through 538 Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 560 through 564 removed outlier: 3.665A pdb=" N THR E 564 " --> pdb=" O SER E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 610 removed outlier: 3.670A pdb=" N GLU E 610 " --> pdb=" O GLU E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 633 Processing helix chain 'E' and resid 681 through 689 removed outlier: 3.831A pdb=" N SER E 685 " --> pdb=" O THR E 681 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 689 " --> pdb=" O SER E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 735 No H-bonds generated for 'chain 'E' and resid 733 through 735' Processing helix chain 'E' and resid 769 through 772 Processing helix chain 'E' and resid 773 through 779 removed outlier: 4.388A pdb=" N PHE E 777 " --> pdb=" O ASP E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 800 Processing helix chain 'E' and resid 850 through 853 Processing helix chain 'E' and resid 919 through 926 Processing helix chain 'E' and resid 933 through 937 removed outlier: 3.516A pdb=" N THR E 937 " --> pdb=" O LEU E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 1029 through 1033 Processing helix chain 'E' and resid 1050 through 1054 Processing helix chain 'E' and resid 1059 through 1063 removed outlier: 4.084A pdb=" N GLU E1063 " --> pdb=" O SER E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1077 through 1081 Processing helix chain 'E' and resid 1129 through 1133 Processing helix chain 'E' and resid 1164 through 1169 removed outlier: 4.287A pdb=" N SER E1168 " --> pdb=" O GLN E1165 " (cutoff:3.500A) Processing helix chain 'E' and resid 1183 through 1188 removed outlier: 3.779A pdb=" N ARG E1187 " --> pdb=" O ALA E1183 " (cutoff:3.500A) Processing helix chain 'E' and resid 1256 through 1259 removed outlier: 3.609A pdb=" N ASP E1259 " --> pdb=" O PRO E1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1256 through 1259' Processing helix chain 'E' and resid 1269 through 1271 No H-bonds generated for 'chain 'E' and resid 1269 through 1271' Processing helix chain 'E' and resid 1291 through 1297 Processing helix chain 'F' and resid 105 through 113 Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 178 through 185 removed outlier: 3.795A pdb=" N LEU F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP F 183 " --> pdb=" O ALA F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.543A pdb=" N ALA F 263 " --> pdb=" O ASP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 288 Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 393 through 398 Processing helix chain 'F' and resid 481 through 484 Processing helix chain 'F' and resid 533 through 538 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.661A pdb=" N THR F 564 " --> pdb=" O SER F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 610 removed outlier: 3.670A pdb=" N GLU F 610 " --> pdb=" O GLU F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 633 Processing helix chain 'F' and resid 681 through 689 removed outlier: 3.826A pdb=" N SER F 685 " --> pdb=" O THR F 681 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR F 689 " --> pdb=" O SER F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 735 No H-bonds generated for 'chain 'F' and resid 733 through 735' Processing helix chain 'F' and resid 769 through 772 Processing helix chain 'F' and resid 773 through 779 removed outlier: 4.419A pdb=" N PHE F 777 " --> pdb=" O ASP F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 800 Processing helix chain 'F' and resid 850 through 853 Processing helix chain 'F' and resid 919 through 926 Processing helix chain 'F' and resid 933 through 937 removed outlier: 3.515A pdb=" N THR F 937 " --> pdb=" O LEU F 934 " (cutoff:3.500A) Processing helix chain 'F' and resid 1029 through 1033 Processing helix chain 'F' and resid 1050 through 1054 Processing helix chain 'F' and resid 1059 through 1063 removed outlier: 4.085A pdb=" N GLU F1063 " --> pdb=" O SER F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1081 Processing helix chain 'F' and resid 1129 through 1133 Processing helix chain 'F' and resid 1164 through 1169 removed outlier: 4.284A pdb=" N SER F1168 " --> pdb=" O GLN F1165 " (cutoff:3.500A) Processing helix chain 'F' and resid 1183 through 1188 removed outlier: 3.777A pdb=" N ARG F1187 " --> pdb=" O ALA F1183 " (cutoff:3.500A) Processing helix chain 'F' and resid 1256 through 1259 removed outlier: 3.606A pdb=" N ASP F1259 " --> pdb=" O PRO F1256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1256 through 1259' Processing helix chain 'F' and resid 1269 through 1271 No H-bonds generated for 'chain 'F' and resid 1269 through 1271' Processing helix chain 'F' and resid 1291 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 43 removed outlier: 9.550A pdb=" N GLN A 229 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR A 101 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR A 231 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 103 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.532A pdb=" N LYS A 245 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 237 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 80 " --> pdb=" O ASN A 244 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 81 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.552A pdb=" N ASP A 313 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 272 removed outlier: 4.034A pdb=" N TYR A 443 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 278 removed outlier: 4.503A pdb=" N LEU A 427 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 461 Processing sheet with id=AA9, first strand: chain 'A' and resid 458 through 461 removed outlier: 8.433A pdb=" N PHE A 789 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 762 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 791 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 764 " --> pdb=" O VAL A 791 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 572 removed outlier: 13.060A pdb=" N MET A 720 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N ARG A 744 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE A 722 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 742 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ALA A 784 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG A 744 " --> pdb=" O ALA A 784 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 675 through 679 removed outlier: 13.060A pdb=" N MET A 720 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N ARG A 744 " --> pdb=" O MET A 720 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE A 722 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 742 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG A 507 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG A 802 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 548 through 549 removed outlier: 6.580A pdb=" N ILE A 639 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER A 669 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 637 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 636 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 700 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 600 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AB5, first strand: chain 'A' and resid 829 through 832 removed outlier: 4.645A pdb=" N ASP A 954 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR A 940 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 836 through 838 removed outlier: 5.871A pdb=" N LEU A 892 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 836 through 838 removed outlier: 5.871A pdb=" N LEU A 892 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 960 through 961 Processing sheet with id=AB9, first strand: chain 'A' and resid 964 through 966 removed outlier: 6.886A pdb=" N THR A 973 " --> pdb=" O SER A 965 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1016 through 1018 removed outlier: 3.731A pdb=" N ASP A1140 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1022 through 1024 removed outlier: 5.552A pdb=" N TYR A1023 " --> pdb=" O ASP A1230 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A1096 " --> pdb=" O TYR A1111 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR A1111 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A1098 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AC4, first strand: chain 'A' and resid 1235 through 1238 removed outlier: 3.677A pdb=" N ARG A1304 " --> pdb=" O GLN A1314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1316 " --> pdb=" O ASP A1302 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP A1302 " --> pdb=" O VAL A1316 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N GLU A1318 " --> pdb=" O PRO A1300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1242 through 1243 Processing sheet with id=AC6, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AC7, first strand: chain 'B' and resid 41 through 43 removed outlier: 9.553A pdb=" N GLN B 229 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 101 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR B 231 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA B 103 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.544A pdb=" N LYS B 245 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 237 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP B 80 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 81 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 264 through 267 removed outlier: 3.559A pdb=" N ASP B 313 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 271 through 272 removed outlier: 4.021A pdb=" N TYR B 443 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 277 through 278 removed outlier: 4.497A pdb=" N LEU B 427 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AD4, first strand: chain 'B' and resid 458 through 461 Processing sheet with id=AD5, first strand: chain 'B' and resid 458 through 461 removed outlier: 8.410A pdb=" N PHE B 789 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 762 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL B 791 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 764 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 569 through 572 removed outlier: 13.036A pdb=" N MET B 720 " --> pdb=" O ARG B 744 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N ARG B 744 " --> pdb=" O MET B 720 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE B 722 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 742 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ALA B 784 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG B 744 " --> pdb=" O ALA B 784 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 675 through 679 removed outlier: 13.036A pdb=" N MET B 720 " --> pdb=" O ARG B 744 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N ARG B 744 " --> pdb=" O MET B 720 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE B 722 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 742 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 507 " --> pdb=" O ARG B 802 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG B 802 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 548 through 549 removed outlier: 6.585A pdb=" N ILE B 639 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER B 669 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 637 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 636 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE B 700 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 600 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AE1, first strand: chain 'B' and resid 829 through 832 removed outlier: 4.651A pdb=" N ASP B 954 " --> pdb=" O THR B 940 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THR B 940 " --> pdb=" O ASP B 954 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 836 through 838 removed outlier: 5.887A pdb=" N LEU B 892 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 836 through 838 removed outlier: 5.887A pdb=" N LEU B 892 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 960 through 961 Processing sheet with id=AE5, first strand: chain 'B' and resid 964 through 966 removed outlier: 6.892A pdb=" N THR B 973 " --> pdb=" O SER B 965 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1016 through 1018 removed outlier: 3.720A pdb=" N ASP B1140 " --> pdb=" O GLU B1150 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1022 through 1024 removed outlier: 5.565A pdb=" N TYR B1023 " --> pdb=" O ASP B1230 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B1096 " --> pdb=" O TYR B1111 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR B1111 " --> pdb=" O LEU B1096 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B1098 " --> pdb=" O LEU B1109 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1162 through 1163 Processing sheet with id=AE9, first strand: chain 'B' and resid 1235 through 1238 removed outlier: 3.678A pdb=" N ARG B1304 " --> pdb=" O GLN B1314 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B1316 " --> pdb=" O ASP B1302 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP B1302 " --> pdb=" O VAL B1316 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLU B1318 " --> pdb=" O PRO B1300 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1242 through 1243 Processing sheet with id=AF2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AF3, first strand: chain 'C' and resid 41 through 43 removed outlier: 9.559A pdb=" N GLN C 229 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR C 101 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR C 231 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA C 103 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.535A pdb=" N LYS C 245 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 237 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP C 80 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 81 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.555A pdb=" N ASP C 313 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 271 through 272 removed outlier: 4.031A pdb=" N TYR C 443 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 277 through 278 removed outlier: 4.488A pdb=" N LEU C 427 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 372 through 373 Processing sheet with id=AF9, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AG1, first strand: chain 'C' and resid 458 through 461 removed outlier: 8.440A pdb=" N PHE C 789 " --> pdb=" O SER C 760 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU C 762 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL C 791 " --> pdb=" O GLU C 762 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 764 " --> pdb=" O VAL C 791 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 569 through 572 removed outlier: 13.020A pdb=" N MET C 720 " --> pdb=" O ARG C 744 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ARG C 744 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE C 722 " --> pdb=" O ILE C 742 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 742 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ALA C 784 " --> pdb=" O ILE C 742 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG C 744 " --> pdb=" O ALA C 784 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 675 through 679 removed outlier: 13.020A pdb=" N MET C 720 " --> pdb=" O ARG C 744 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ARG C 744 " --> pdb=" O MET C 720 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE C 722 " --> pdb=" O ILE C 742 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 742 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG C 507 " --> pdb=" O ARG C 802 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG C 802 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 548 through 549 removed outlier: 6.590A pdb=" N ILE C 639 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER C 669 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 637 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 636 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE C 700 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 600 " --> pdb=" O ILE C 700 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AG6, first strand: chain 'C' and resid 829 through 832 removed outlier: 4.684A pdb=" N ASP C 954 " --> pdb=" O THR C 940 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR C 940 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 836 through 838 removed outlier: 5.798A pdb=" N LEU C 892 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 836 through 838 removed outlier: 5.798A pdb=" N LEU C 892 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 960 through 961 Processing sheet with id=AH1, first strand: chain 'C' and resid 964 through 966 removed outlier: 6.894A pdb=" N THR C 973 " --> pdb=" O SER C 965 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1016 through 1018 removed outlier: 3.715A pdb=" N ASP C1140 " --> pdb=" O GLU C1150 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1022 through 1024 removed outlier: 5.558A pdb=" N TYR C1023 " --> pdb=" O ASP C1230 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C1096 " --> pdb=" O TYR C1111 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR C1111 " --> pdb=" O LEU C1096 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE C1098 " --> pdb=" O LEU C1109 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1162 through 1163 Processing sheet with id=AH5, first strand: chain 'C' and resid 1235 through 1238 removed outlier: 3.679A pdb=" N ARG C1304 " --> pdb=" O GLN C1314 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C1316 " --> pdb=" O ASP C1302 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP C1302 " --> pdb=" O VAL C1316 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N GLU C1318 " --> pdb=" O PRO C1300 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1242 through 1243 Processing sheet with id=AH7, first strand: chain 'D' and resid 41 through 43 Processing sheet with id=AH8, first strand: chain 'D' and resid 41 through 43 removed outlier: 9.549A pdb=" N GLN D 229 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR D 101 " --> pdb=" O GLN D 229 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR D 231 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA D 103 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.532A pdb=" N LYS D 245 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 237 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP D 80 " --> pdb=" O ASN D 244 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL D 81 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 264 through 267 removed outlier: 3.551A pdb=" N ASP D 313 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 271 through 272 removed outlier: 4.034A pdb=" N TYR D 443 " --> pdb=" O THR D 446 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 277 through 278 removed outlier: 4.503A pdb=" N LEU D 427 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 372 through 373 Processing sheet with id=AI5, first strand: chain 'D' and resid 458 through 461 Processing sheet with id=AI6, first strand: chain 'D' and resid 458 through 461 removed outlier: 8.432A pdb=" N PHE D 789 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU D 762 " --> pdb=" O PHE D 789 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL D 791 " --> pdb=" O GLU D 762 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 764 " --> pdb=" O VAL D 791 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 569 through 572 removed outlier: 13.061A pdb=" N MET D 720 " --> pdb=" O ARG D 744 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ARG D 744 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N PHE D 722 " --> pdb=" O ILE D 742 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 742 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ALA D 784 " --> pdb=" O ILE D 742 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG D 744 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 675 through 679 removed outlier: 13.061A pdb=" N MET D 720 " --> pdb=" O ARG D 744 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ARG D 744 " --> pdb=" O MET D 720 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N PHE D 722 " --> pdb=" O ILE D 742 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE D 742 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 507 " --> pdb=" O ARG D 802 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG D 802 " --> pdb=" O ARG D 507 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 548 through 549 removed outlier: 6.580A pdb=" N ILE D 639 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER D 669 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 637 " --> pdb=" O SER D 669 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 636 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 700 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 600 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AJ2, first strand: chain 'D' and resid 829 through 832 removed outlier: 4.645A pdb=" N ASP D 954 " --> pdb=" O THR D 940 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR D 940 " --> pdb=" O ASP D 954 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 836 through 838 removed outlier: 5.871A pdb=" N LEU D 892 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 836 through 838 removed outlier: 5.871A pdb=" N LEU D 892 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 960 through 961 Processing sheet with id=AJ6, first strand: chain 'D' and resid 964 through 966 removed outlier: 6.887A pdb=" N THR D 973 " --> pdb=" O SER D 965 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 1016 through 1018 removed outlier: 3.734A pdb=" N ASP D1140 " --> pdb=" O GLU D1150 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 1022 through 1024 removed outlier: 5.550A pdb=" N TYR D1023 " --> pdb=" O ASP D1230 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D1096 " --> pdb=" O TYR D1111 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR D1111 " --> pdb=" O LEU D1096 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE D1098 " --> pdb=" O LEU D1109 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 1162 through 1163 Processing sheet with id=AK1, first strand: chain 'D' and resid 1235 through 1238 removed outlier: 3.678A pdb=" N ARG D1304 " --> pdb=" O GLN D1314 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D1316 " --> pdb=" O ASP D1302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP D1302 " --> pdb=" O VAL D1316 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLU D1318 " --> pdb=" O PRO D1300 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 1242 through 1243 Processing sheet with id=AK3, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AK4, first strand: chain 'E' and resid 41 through 43 removed outlier: 9.552A pdb=" N GLN E 229 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR E 101 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR E 231 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA E 103 " --> pdb=" O TYR E 231 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.544A pdb=" N LYS E 245 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 237 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP E 80 " --> pdb=" O ASN E 244 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 81 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 264 through 267 removed outlier: 3.559A pdb=" N ASP E 313 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 271 through 272 removed outlier: 4.021A pdb=" N TYR E 443 " --> pdb=" O THR E 446 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'E' and resid 277 through 278 removed outlier: 4.497A pdb=" N LEU E 427 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'E' and resid 372 through 373 Processing sheet with id=AL1, first strand: chain 'E' and resid 458 through 461 Processing sheet with id=AL2, first strand: chain 'E' and resid 458 through 461 removed outlier: 8.412A pdb=" N PHE E 789 " --> pdb=" O SER E 760 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU E 762 " --> pdb=" O PHE E 789 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 791 " --> pdb=" O GLU E 762 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL E 764 " --> pdb=" O VAL E 791 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'E' and resid 569 through 572 removed outlier: 13.035A pdb=" N MET E 720 " --> pdb=" O ARG E 744 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N ARG E 744 " --> pdb=" O MET E 720 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE E 722 " --> pdb=" O ILE E 742 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 742 " --> pdb=" O PHE E 722 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ALA E 784 " --> pdb=" O ILE E 742 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG E 744 " --> pdb=" O ALA E 784 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 675 through 679 removed outlier: 13.035A pdb=" N MET E 720 " --> pdb=" O ARG E 744 " (cutoff:3.500A) removed outlier: 12.228A pdb=" N ARG E 744 " --> pdb=" O MET E 720 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE E 722 " --> pdb=" O ILE E 742 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 742 " --> pdb=" O PHE E 722 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG E 507 " --> pdb=" O ARG E 802 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ARG E 802 " --> pdb=" O ARG E 507 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'E' and resid 548 through 549 removed outlier: 6.585A pdb=" N ILE E 639 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER E 669 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 637 " --> pdb=" O SER E 669 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 636 " --> pdb=" O THR E 707 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE E 700 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 600 " --> pdb=" O ILE E 700 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'E' and resid 527 through 529 Processing sheet with id=AL7, first strand: chain 'E' and resid 829 through 832 removed outlier: 4.652A pdb=" N ASP E 954 " --> pdb=" O THR E 940 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR E 940 " --> pdb=" O ASP E 954 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'E' and resid 836 through 838 removed outlier: 5.889A pdb=" N LEU E 892 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'E' and resid 836 through 838 removed outlier: 5.889A pdb=" N LEU E 892 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'E' and resid 960 through 961 Processing sheet with id=AM2, first strand: chain 'E' and resid 964 through 966 removed outlier: 6.891A pdb=" N THR E 973 " --> pdb=" O SER E 965 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'E' and resid 1016 through 1018 removed outlier: 3.721A pdb=" N ASP E1140 " --> pdb=" O GLU E1150 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'E' and resid 1022 through 1024 removed outlier: 5.565A pdb=" N TYR E1023 " --> pdb=" O ASP E1230 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E1096 " --> pdb=" O TYR E1111 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR E1111 " --> pdb=" O LEU E1096 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E1098 " --> pdb=" O LEU E1109 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 1162 through 1163 Processing sheet with id=AM6, first strand: chain 'E' and resid 1235 through 1238 removed outlier: 3.678A pdb=" N ARG E1304 " --> pdb=" O GLN E1314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E1316 " --> pdb=" O ASP E1302 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP E1302 " --> pdb=" O VAL E1316 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLU E1318 " --> pdb=" O PRO E1300 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'E' and resid 1242 through 1243 Processing sheet with id=AM8, first strand: chain 'F' and resid 41 through 43 Processing sheet with id=AM9, first strand: chain 'F' and resid 41 through 43 removed outlier: 9.560A pdb=" N GLN F 229 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR F 101 " --> pdb=" O GLN F 229 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR F 231 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA F 103 " --> pdb=" O TYR F 231 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.536A pdb=" N LYS F 245 " --> pdb=" O GLY F 248 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY F 237 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP F 80 " --> pdb=" O ASN F 244 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL F 81 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.555A pdb=" N ASP F 313 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'F' and resid 271 through 272 removed outlier: 4.031A pdb=" N TYR F 443 " --> pdb=" O THR F 446 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'F' and resid 277 through 278 removed outlier: 4.487A pdb=" N LEU F 427 " --> pdb=" O VAL F 278 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'F' and resid 372 through 373 Processing sheet with id=AN6, first strand: chain 'F' and resid 458 through 461 Processing sheet with id=AN7, first strand: chain 'F' and resid 458 through 461 removed outlier: 8.440A pdb=" N PHE F 789 " --> pdb=" O SER F 760 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU F 762 " --> pdb=" O PHE F 789 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL F 791 " --> pdb=" O GLU F 762 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 764 " --> pdb=" O VAL F 791 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'F' and resid 569 through 572 removed outlier: 13.020A pdb=" N MET F 720 " --> pdb=" O ARG F 744 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ARG F 744 " --> pdb=" O MET F 720 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE F 722 " --> pdb=" O ILE F 742 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 742 " --> pdb=" O PHE F 722 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ALA F 784 " --> pdb=" O ILE F 742 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG F 744 " --> pdb=" O ALA F 784 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'F' and resid 675 through 679 removed outlier: 13.020A pdb=" N MET F 720 " --> pdb=" O ARG F 744 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ARG F 744 " --> pdb=" O MET F 720 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE F 722 " --> pdb=" O ILE F 742 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 742 " --> pdb=" O PHE F 722 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG F 507 " --> pdb=" O ARG F 802 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG F 802 " --> pdb=" O ARG F 507 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'F' and resid 548 through 549 removed outlier: 6.590A pdb=" N ILE F 639 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER F 669 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 637 " --> pdb=" O SER F 669 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 636 " --> pdb=" O THR F 707 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE F 700 " --> pdb=" O LEU F 600 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU F 600 " --> pdb=" O ILE F 700 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'F' and resid 527 through 529 Processing sheet with id=AO3, first strand: chain 'F' and resid 829 through 832 removed outlier: 4.684A pdb=" N ASP F 954 " --> pdb=" O THR F 940 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR F 940 " --> pdb=" O ASP F 954 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'F' and resid 836 through 838 removed outlier: 5.797A pdb=" N LEU F 892 " --> pdb=" O VAL F 991 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'F' and resid 836 through 838 removed outlier: 5.797A pdb=" N LEU F 892 " --> pdb=" O VAL F 991 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'F' and resid 960 through 961 Processing sheet with id=AO7, first strand: chain 'F' and resid 964 through 966 removed outlier: 6.894A pdb=" N THR F 973 " --> pdb=" O SER F 965 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'F' and resid 1016 through 1018 removed outlier: 3.715A pdb=" N ASP F1140 " --> pdb=" O GLU F1150 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'F' and resid 1022 through 1024 removed outlier: 5.556A pdb=" N TYR F1023 " --> pdb=" O ASP F1230 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU F1096 " --> pdb=" O TYR F1111 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR F1111 " --> pdb=" O LEU F1096 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE F1098 " --> pdb=" O LEU F1109 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'F' and resid 1162 through 1163 Processing sheet with id=AP2, first strand: chain 'F' and resid 1235 through 1238 removed outlier: 3.680A pdb=" N ARG F1304 " --> pdb=" O GLN F1314 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F1316 " --> pdb=" O ASP F1302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP F1302 " --> pdb=" O VAL F1316 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLU F1318 " --> pdb=" O PRO F1300 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'F' and resid 1242 through 1243 1926 hydrogen bonds defined for protein. 4644 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: 37.66 Time building geometry restraints manager: 12.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 1731 1.22 - 1.38: 20361 1.38 - 1.54: 36980 1.54 - 1.69: 760 1.69 - 1.85: 168 Bond restraints: 60000 Sorted by residual: bond pdb=" C LEU F 858 " pdb=" O LEU F 858 " ideal model delta sigma weight residual 1.234 1.068 0.166 1.22e-02 6.72e+03 1.86e+02 bond pdb=" C LEU C 858 " pdb=" O LEU C 858 " ideal model delta sigma weight residual 1.234 1.069 0.166 1.22e-02 6.72e+03 1.85e+02 bond pdb=" C LEU D 858 " pdb=" O LEU D 858 " ideal model delta sigma weight residual 1.234 1.080 0.155 1.22e-02 6.72e+03 1.61e+02 bond pdb=" C LEU A 858 " pdb=" O LEU A 858 " ideal model delta sigma weight residual 1.234 1.082 0.153 1.22e-02 6.72e+03 1.57e+02 bond pdb=" C LEU B 858 " pdb=" O LEU B 858 " ideal model delta sigma weight residual 1.234 1.088 0.147 1.22e-02 6.72e+03 1.45e+02 ... (remaining 59995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 80080 3.63 - 7.27: 1906 7.27 - 10.90: 65 10.90 - 14.54: 15 14.54 - 18.17: 2 Bond angle restraints: 82068 Sorted by residual: angle pdb=" CA ASP A 729 " pdb=" CB ASP A 729 " pdb=" CG ASP A 729 " ideal model delta sigma weight residual 112.60 130.77 -18.17 1.00e+00 1.00e+00 3.30e+02 angle pdb=" C GLN D 58 " pdb=" CA GLN D 58 " pdb=" CB GLN D 58 " ideal model delta sigma weight residual 109.70 96.00 13.70 1.61e+00 3.86e-01 7.24e+01 angle pdb=" C GLN A 58 " pdb=" CA GLN A 58 " pdb=" CB GLN A 58 " ideal model delta sigma weight residual 109.70 96.03 13.67 1.61e+00 3.86e-01 7.21e+01 angle pdb=" C GLN C 58 " pdb=" CA GLN C 58 " pdb=" CB GLN C 58 " ideal model delta sigma weight residual 109.70 96.20 13.50 1.61e+00 3.86e-01 7.03e+01 angle pdb=" C GLN B 58 " pdb=" CA GLN B 58 " pdb=" CB GLN B 58 " ideal model delta sigma weight residual 109.70 97.01 12.69 1.61e+00 3.86e-01 6.22e+01 ... (remaining 82063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 32315 17.77 - 35.53: 2613 35.53 - 53.30: 357 53.30 - 71.06: 104 71.06 - 88.83: 53 Dihedral angle restraints: 35442 sinusoidal: 12762 harmonic: 22680 Sorted by residual: dihedral pdb=" C GLN D 58 " pdb=" N GLN D 58 " pdb=" CA GLN D 58 " pdb=" CB GLN D 58 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C GLN C 58 " pdb=" N GLN C 58 " pdb=" CA GLN C 58 " pdb=" CB GLN C 58 " ideal model delta harmonic sigma weight residual -122.60 -106.82 -15.78 0 2.50e+00 1.60e-01 3.98e+01 dihedral pdb=" C GLN A 58 " pdb=" N GLN A 58 " pdb=" CA GLN A 58 " pdb=" CB GLN A 58 " ideal model delta harmonic sigma weight residual -122.60 -106.84 -15.76 0 2.50e+00 1.60e-01 3.97e+01 ... (remaining 35439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 6108 0.076 - 0.153: 3156 0.153 - 0.229: 449 0.229 - 0.306: 70 0.306 - 0.382: 15 Chirality restraints: 9798 Sorted by residual: chirality pdb=" CA ASN A 550 " pdb=" N ASN A 550 " pdb=" C ASN A 550 " pdb=" CB ASN A 550 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN B 550 " pdb=" N ASN B 550 " pdb=" C ASN B 550 " pdb=" CB ASN B 550 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA ASN F 38 " pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CB ASN F 38 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 9795 not shown) Planarity restraints: 11058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 196 " -0.044 2.00e-02 2.50e+03 9.21e-02 8.48e+01 pdb=" CD GLU A 196 " 0.159 2.00e-02 2.50e+03 pdb=" OE1 GLU A 196 " -0.059 2.00e-02 2.50e+03 pdb=" OE2 GLU A 196 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 729 " -0.041 2.00e-02 2.50e+03 7.57e-02 5.73e+01 pdb=" CG ASP A 729 " 0.131 2.00e-02 2.50e+03 pdb=" OD1 ASP A 729 " -0.049 2.00e-02 2.50e+03 pdb=" OD2 ASP A 729 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 55 " 0.030 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C SER B 55 " -0.111 2.00e-02 2.50e+03 pdb=" O SER B 55 " 0.041 2.00e-02 2.50e+03 pdb=" N GLY B 56 " 0.039 2.00e-02 2.50e+03 ... (remaining 11055 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 18 1.90 - 2.65: 1192 2.65 - 3.40: 77860 3.40 - 4.15: 148135 4.15 - 4.90: 265397 Nonbonded interactions: 492602 Sorted by model distance: nonbonded pdb=" OE1 GLU A 196 " pdb=" OE1 GLU F 143 " model vdw 1.144 3.040 nonbonded pdb=" OE1 GLU A 143 " pdb=" OE1 GLU B 196 " model vdw 1.276 3.040 nonbonded pdb=" OE1 GLU C 143 " pdb=" OE1 GLU D 196 " model vdw 1.277 3.040 nonbonded pdb=" OE1 GLU D 143 " pdb=" OE1 GLU E 196 " model vdw 1.277 3.040 nonbonded pdb=" OE2 GLU A1087 " pdb=" CZ ARG F 802 " model vdw 1.278 3.270 ... (remaining 492597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 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: 0.060 Extract box with map and model: 1.620 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 119.860 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.014 0.179 60000 Z= 0.934 Angle : 1.588 18.173 82068 Z= 1.110 Chirality : 0.084 0.382 9798 Planarity : 0.008 0.092 11058 Dihedral : 13.757 88.830 20814 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.76 % Allowed : 4.23 % Favored : 95.02 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 7950 helix: -2.69 (0.16), residues: 600 sheet: 0.55 (0.11), residues: 2210 loop : -1.14 (0.08), residues: 5140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.010 TRP E 286 HIS 0.017 0.005 HIS D 826 PHE 0.039 0.008 PHE F1303 TYR 0.049 0.008 TYR D 763 ARG 0.033 0.003 ARG D 802 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1105 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 SER cc_start: 0.7992 (p) cc_final: 0.7738 (t) REVERT: A 350 ASP cc_start: 0.7840 (t0) cc_final: 0.7594 (t0) REVERT: A 393 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 445 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 559 ARG cc_start: 0.7109 (mmt90) cc_final: 0.5757 (mtt180) REVERT: A 606 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7790 (mt-10) REVERT: A 786 ASP cc_start: 0.8798 (p0) cc_final: 0.8550 (p0) REVERT: A 898 ASP cc_start: 0.8024 (t0) cc_final: 0.7816 (t0) REVERT: A 992 ASP cc_start: 0.7146 (t0) cc_final: 0.6910 (t0) REVERT: A 1105 ASP cc_start: 0.7058 (t0) cc_final: 0.6470 (m-30) REVERT: A 1170 ASP cc_start: 0.7525 (m-30) cc_final: 0.7037 (t0) REVERT: A 1202 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 1327 LYS cc_start: 0.7813 (mttt) cc_final: 0.7517 (mmtp) REVERT: A 1330 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.4037 (ttt-90) REVERT: B 46 GLU cc_start: 0.8536 (tt0) cc_final: 0.8305 (tt0) REVERT: B 51 ASP cc_start: 0.8123 (t70) cc_final: 0.7785 (m-30) REVERT: B 74 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 232 GLU cc_start: 0.8118 (tp30) cc_final: 0.7492 (mm-30) REVERT: B 264 GLU cc_start: 0.8059 (pt0) cc_final: 0.7569 (tt0) REVERT: B 306 THR cc_start: 0.8054 (p) cc_final: 0.7844 (t) REVERT: B 340 MET cc_start: 0.9207 (mtp) cc_final: 0.8780 (mtp) REVERT: B 375 ASN cc_start: 0.6988 (t0) cc_final: 0.6771 (t160) REVERT: B 409 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7379 (mt0) REVERT: B 467 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8236 (mt-10) REVERT: B 472 GLN cc_start: 0.7102 (mt0) cc_final: 0.6893 (mm110) REVERT: B 473 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8362 (tp30) REVERT: B 543 THR cc_start: 0.8478 (m) cc_final: 0.8138 (p) REVERT: B 559 ARG cc_start: 0.7253 (mmt90) cc_final: 0.6270 (mtt180) REVERT: B 635 ASP cc_start: 0.8404 (m-30) cc_final: 0.8200 (m-30) REVERT: B 737 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8082 (mtt180) REVERT: B 765 MET cc_start: 0.8728 (tpp) cc_final: 0.8286 (tpp) REVERT: B 874 ASP cc_start: 0.8105 (m-30) cc_final: 0.7769 (m-30) REVERT: B 898 ASP cc_start: 0.7488 (t0) cc_final: 0.7054 (t70) REVERT: B 987 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7815 (mt-10) REVERT: B 999 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6293 (mt-10) REVERT: B 1021 THR cc_start: 0.7943 (m) cc_final: 0.7671 (p) REVERT: B 1120 LYS cc_start: 0.7586 (mttt) cc_final: 0.6722 (ttmm) REVERT: B 1284 MET cc_start: 0.8291 (mtp) cc_final: 0.8021 (mtp) REVERT: B 1318 GLU cc_start: 0.7053 (tt0) cc_final: 0.6212 (tp30) REVERT: B 1327 LYS cc_start: 0.7811 (mttt) cc_final: 0.7187 (pttt) REVERT: B 1330 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.5627 (mmt-90) REVERT: B 1354 GLU cc_start: 0.7657 (tt0) cc_final: 0.6871 (mt-10) REVERT: C 51 ASP cc_start: 0.8719 (t70) cc_final: 0.8315 (m-30) REVERT: C 71 ASP cc_start: 0.8675 (p0) cc_final: 0.8135 (m-30) REVERT: C 74 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7454 (mt-10) REVERT: C 116 THR cc_start: 0.8100 (m) cc_final: 0.7533 (p) REVERT: C 264 GLU cc_start: 0.8236 (pt0) cc_final: 0.7946 (pm20) REVERT: C 422 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8158 (m) REVERT: C 460 ASP cc_start: 0.8177 (t70) cc_final: 0.7838 (t70) REVERT: C 472 GLN cc_start: 0.7956 (mt0) cc_final: 0.7362 (mm-40) REVERT: C 515 ASP cc_start: 0.8444 (p0) cc_final: 0.8211 (p0) REVERT: C 565 ASN cc_start: 0.7322 (OUTLIER) cc_final: 0.6942 (p0) REVERT: C 693 ASN cc_start: 0.7171 (m-40) cc_final: 0.6891 (m110) REVERT: C 729 ASP cc_start: 0.7275 (t70) cc_final: 0.7066 (t70) REVERT: C 797 ASP cc_start: 0.8591 (t0) cc_final: 0.8387 (t70) REVERT: C 799 ASP cc_start: 0.7955 (m-30) cc_final: 0.7748 (m-30) REVERT: C 885 SER cc_start: 0.8404 (t) cc_final: 0.8113 (p) REVERT: C 999 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: C 1091 ASP cc_start: 0.6833 (m-30) cc_final: 0.6233 (p0) REVERT: C 1101 ILE cc_start: 0.7521 (pt) cc_final: 0.6761 (pt) REVERT: C 1138 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6198 (pp20) REVERT: C 1156 LYS cc_start: 0.7561 (mtpp) cc_final: 0.7100 (mttt) REVERT: C 1182 LYS cc_start: 0.7337 (mppt) cc_final: 0.7089 (mtmm) REVERT: C 1225 ASP cc_start: 0.7527 (t0) cc_final: 0.7324 (t0) REVERT: C 1230 ASP cc_start: 0.6725 (t0) cc_final: 0.6320 (t0) REVERT: C 1272 LEU cc_start: 0.8277 (mt) cc_final: 0.7719 (mm) REVERT: C 1318 GLU cc_start: 0.6789 (tt0) cc_final: 0.6325 (tt0) REVERT: C 1347 ASP cc_start: 0.7225 (m-30) cc_final: 0.6701 (t0) REVERT: D 174 THR cc_start: 0.8558 (p) cc_final: 0.8356 (t) REVERT: D 308 SER cc_start: 0.7990 (p) cc_final: 0.7735 (t) REVERT: D 350 ASP cc_start: 0.7838 (t0) cc_final: 0.7593 (t0) REVERT: D 393 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 408 GLU cc_start: 0.7523 (tt0) cc_final: 0.7316 (tt0) REVERT: D 523 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8453 (pt) REVERT: D 559 ARG cc_start: 0.7107 (mmt90) cc_final: 0.5773 (mtt90) REVERT: D 606 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7825 (mt-10) REVERT: D 786 ASP cc_start: 0.8799 (p0) cc_final: 0.8559 (p0) REVERT: D 898 ASP cc_start: 0.8023 (t0) cc_final: 0.7816 (t0) REVERT: D 992 ASP cc_start: 0.7232 (t0) cc_final: 0.6973 (t0) REVERT: D 1105 ASP cc_start: 0.7039 (t0) cc_final: 0.6445 (m-30) REVERT: D 1170 ASP cc_start: 0.7531 (m-30) cc_final: 0.7046 (t0) REVERT: D 1202 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7515 (tm-30) REVERT: D 1330 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.4509 (mmt-90) REVERT: E 46 GLU cc_start: 0.8538 (tt0) cc_final: 0.8306 (tt0) REVERT: E 51 ASP cc_start: 0.8133 (t70) cc_final: 0.7787 (m-30) REVERT: E 74 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7323 (mt-10) REVERT: E 232 GLU cc_start: 0.8121 (tp30) cc_final: 0.7508 (mm-30) REVERT: E 264 GLU cc_start: 0.8056 (pt0) cc_final: 0.7567 (tt0) REVERT: E 306 THR cc_start: 0.8055 (p) cc_final: 0.7848 (t) REVERT: E 340 MET cc_start: 0.9211 (mtp) cc_final: 0.8746 (mtp) REVERT: E 375 ASN cc_start: 0.6987 (t0) cc_final: 0.6772 (t160) REVERT: E 409 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7380 (mt0) REVERT: E 467 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8222 (mt-10) REVERT: E 472 GLN cc_start: 0.7100 (mt0) cc_final: 0.6888 (mm110) REVERT: E 473 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8365 (tp30) REVERT: E 543 THR cc_start: 0.8482 (m) cc_final: 0.8141 (p) REVERT: E 559 ARG cc_start: 0.7257 (mmt90) cc_final: 0.6272 (mtt180) REVERT: E 635 ASP cc_start: 0.8403 (m-30) cc_final: 0.8198 (m-30) REVERT: E 765 MET cc_start: 0.8726 (tpp) cc_final: 0.8280 (tpp) REVERT: E 874 ASP cc_start: 0.8105 (m-30) cc_final: 0.7772 (m-30) REVERT: E 898 ASP cc_start: 0.7487 (t0) cc_final: 0.7053 (t70) REVERT: E 987 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7818 (mt-10) REVERT: E 999 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6568 (mm-30) REVERT: E 1021 THR cc_start: 0.7965 (m) cc_final: 0.7695 (p) REVERT: E 1120 LYS cc_start: 0.7580 (mttt) cc_final: 0.6715 (ttmm) REVERT: E 1284 MET cc_start: 0.8295 (mtp) cc_final: 0.8025 (mtp) REVERT: E 1318 GLU cc_start: 0.7048 (tt0) cc_final: 0.6224 (tp30) REVERT: E 1327 LYS cc_start: 0.7813 (mttt) cc_final: 0.7198 (pttt) REVERT: E 1330 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.5696 (mmt-90) REVERT: E 1354 GLU cc_start: 0.7656 (tt0) cc_final: 0.6871 (mt-10) REVERT: F 51 ASP cc_start: 0.8739 (t70) cc_final: 0.8366 (m-30) REVERT: F 71 ASP cc_start: 0.8707 (p0) cc_final: 0.8174 (m-30) REVERT: F 74 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7455 (mt-10) REVERT: F 116 THR cc_start: 0.8100 (m) cc_final: 0.7536 (p) REVERT: F 264 GLU cc_start: 0.8236 (pt0) cc_final: 0.7947 (pm20) REVERT: F 275 VAL cc_start: 0.8600 (t) cc_final: 0.8399 (p) REVERT: F 422 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8165 (m) REVERT: F 460 ASP cc_start: 0.8180 (t70) cc_final: 0.7842 (t70) REVERT: F 472 GLN cc_start: 0.7956 (mt0) cc_final: 0.7358 (mm-40) REVERT: F 499 ASP cc_start: 0.8404 (m-30) cc_final: 0.8008 (m-30) REVERT: F 515 ASP cc_start: 0.8445 (p0) cc_final: 0.8213 (p0) REVERT: F 565 ASN cc_start: 0.7366 (OUTLIER) cc_final: 0.6992 (p0) REVERT: F 693 ASN cc_start: 0.7172 (m-40) cc_final: 0.6892 (m110) REVERT: F 797 ASP cc_start: 0.8593 (t0) cc_final: 0.8387 (t70) REVERT: F 799 ASP cc_start: 0.7953 (m-30) cc_final: 0.7749 (m-30) REVERT: F 885 SER cc_start: 0.8500 (t) cc_final: 0.8128 (p) REVERT: F 1091 ASP cc_start: 0.6833 (m-30) cc_final: 0.6238 (p0) REVERT: F 1101 ILE cc_start: 0.7518 (pt) cc_final: 0.6757 (pt) REVERT: F 1138 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6206 (pp20) REVERT: F 1139 MET cc_start: 0.8072 (mtm) cc_final: 0.7859 (mtp) REVERT: F 1156 LYS cc_start: 0.7485 (mtpp) cc_final: 0.7010 (mttt) REVERT: F 1182 LYS cc_start: 0.7340 (mppt) cc_final: 0.7092 (mtmm) REVERT: F 1225 ASP cc_start: 0.7526 (t0) cc_final: 0.7324 (t0) REVERT: F 1230 ASP cc_start: 0.6729 (t0) cc_final: 0.6333 (t0) REVERT: F 1272 LEU cc_start: 0.8273 (mt) cc_final: 0.7728 (mm) REVERT: F 1318 GLU cc_start: 0.6803 (tt0) cc_final: 0.6331 (tt0) REVERT: F 1347 ASP cc_start: 0.7226 (m-30) cc_final: 0.6696 (t0) outliers start: 50 outliers final: 12 residues processed: 1148 average time/residue: 1.1544 time to fit residues: 1763.1686 Evaluate side-chains 583 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 560 time to evaluate : 4.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain B residue 269 ARG Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 1330 ARG Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 565 ASN Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 269 ARG Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 999 GLU Chi-restraints excluded: chain E residue 1330 ARG Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 565 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 0.9990 chunk 600 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 404 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 620 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 chunk 719 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 58 GLN A 92 GLN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 733 GLN A 804 ASN A 956 GLN B 58 GLN B 84 ASN B 92 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 244 ASN B 472 GLN B 565 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 663 ASN B 693 ASN B 697 ASN B 804 ASN B 956 GLN B1050 HIS C 38 ASN C 58 GLN C 84 ASN C 92 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN C 804 ASN C 868 ASN C1050 HIS D 38 ASN D 58 GLN D 92 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 ASN D 693 ASN D 733 GLN D 804 ASN D 956 GLN E 58 GLN E 70 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN E 244 ASN E 565 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 ASN E 663 ASN E 693 ASN E 697 ASN E 804 ASN E 956 GLN E1050 HIS F 58 GLN F 84 ASN F 92 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN ** F 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 733 GLN F 804 ASN F 868 ASN F 956 GLN F1050 HIS Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 60000 Z= 0.147 Angle : 0.532 6.912 82068 Z= 0.295 Chirality : 0.045 0.165 9798 Planarity : 0.004 0.041 11058 Dihedral : 5.359 82.301 8362 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.76 % Allowed : 10.38 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 7950 helix: -2.24 (0.18), residues: 612 sheet: 0.89 (0.11), residues: 2342 loop : -0.74 (0.08), residues: 4996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1275 HIS 0.004 0.001 HIS B1050 PHE 0.014 0.001 PHE C 102 TYR 0.015 0.001 TYR F1348 ARG 0.003 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 690 time to evaluate : 4.968 Fit side-chains REVERT: A 321 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: A 337 SER cc_start: 0.8218 (m) cc_final: 0.7937 (p) REVERT: A 421 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 467 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7586 (pt0) REVERT: A 559 ARG cc_start: 0.7131 (mmt90) cc_final: 0.5748 (mtt180) REVERT: A 606 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7566 (mt-10) REVERT: A 610 GLU cc_start: 0.6156 (pt0) cc_final: 0.5868 (pt0) REVERT: A 617 ASN cc_start: 0.8591 (m110) cc_final: 0.8323 (m-40) REVERT: A 673 ASN cc_start: 0.8033 (m-40) cc_final: 0.7340 (t160) REVERT: A 786 ASP cc_start: 0.8720 (p0) cc_final: 0.8449 (p0) REVERT: A 898 ASP cc_start: 0.7792 (t0) cc_final: 0.7549 (t0) REVERT: A 1090 MET cc_start: 0.7861 (tmm) cc_final: 0.7499 (tmm) REVERT: A 1170 ASP cc_start: 0.7571 (m-30) cc_final: 0.7197 (m-30) REVERT: A 1262 ASN cc_start: 0.7197 (p0) cc_final: 0.6829 (p0) REVERT: A 1327 LYS cc_start: 0.7876 (mttt) cc_final: 0.7633 (mmtp) REVERT: A 1354 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: B 38 ASN cc_start: 0.6923 (m110) cc_final: 0.6715 (m110) REVERT: B 46 GLU cc_start: 0.8587 (tt0) cc_final: 0.8367 (tt0) REVERT: B 51 ASP cc_start: 0.8020 (t70) cc_final: 0.7747 (m-30) REVERT: B 264 GLU cc_start: 0.8105 (pt0) cc_final: 0.7602 (tt0) REVERT: B 375 ASN cc_start: 0.6885 (t0) cc_final: 0.6616 (t0) REVERT: B 409 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7201 (mt0) REVERT: B 467 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8066 (mt-10) REVERT: B 472 GLN cc_start: 0.6862 (mt0) cc_final: 0.6634 (mm110) REVERT: B 543 THR cc_start: 0.8590 (m) cc_final: 0.8294 (p) REVERT: B 559 ARG cc_start: 0.7442 (mmt90) cc_final: 0.6389 (mtt180) REVERT: B 695 ASP cc_start: 0.7358 (p0) cc_final: 0.6815 (m-30) REVERT: B 765 MET cc_start: 0.8603 (tpp) cc_final: 0.8205 (tpp) REVERT: B 874 ASP cc_start: 0.8217 (m-30) cc_final: 0.7904 (m-30) REVERT: B 898 ASP cc_start: 0.7358 (t0) cc_final: 0.6965 (t70) REVERT: B 987 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7248 (mp0) REVERT: B 1019 ASP cc_start: 0.5983 (t0) cc_final: 0.5427 (t70) REVERT: B 1032 ASP cc_start: 0.6337 (m-30) cc_final: 0.6066 (m-30) REVERT: B 1120 LYS cc_start: 0.7606 (mttt) cc_final: 0.6734 (ttmm) REVERT: B 1262 ASN cc_start: 0.7154 (p0) cc_final: 0.6942 (p0) REVERT: B 1318 GLU cc_start: 0.7182 (tt0) cc_final: 0.6324 (tp30) REVERT: B 1327 LYS cc_start: 0.7853 (mttt) cc_final: 0.7246 (pttt) REVERT: B 1354 GLU cc_start: 0.7484 (tt0) cc_final: 0.6827 (mt-10) REVERT: C 51 ASP cc_start: 0.8586 (t70) cc_final: 0.8234 (m-30) REVERT: C 71 ASP cc_start: 0.8516 (p0) cc_final: 0.8142 (m-30) REVERT: C 74 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 116 THR cc_start: 0.7501 (m) cc_final: 0.7079 (p) REVERT: C 472 GLN cc_start: 0.7646 (mt0) cc_final: 0.7102 (mm-40) REVERT: C 499 ASP cc_start: 0.8241 (m-30) cc_final: 0.7885 (m-30) REVERT: C 606 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7384 (tt0) REVERT: C 693 ASN cc_start: 0.7027 (m-40) cc_final: 0.6807 (m110) REVERT: C 885 SER cc_start: 0.8657 (t) cc_final: 0.8367 (p) REVERT: C 1091 ASP cc_start: 0.6691 (m-30) cc_final: 0.6127 (p0) REVERT: C 1138 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6398 (pp20) REVERT: C 1182 LYS cc_start: 0.7545 (mppt) cc_final: 0.7272 (mtmm) REVERT: C 1276 ASP cc_start: 0.7125 (t0) cc_final: 0.6908 (t0) REVERT: C 1318 GLU cc_start: 0.6785 (tt0) cc_final: 0.6369 (tt0) REVERT: D 321 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6034 (pm20) REVERT: D 337 SER cc_start: 0.8220 (m) cc_final: 0.7940 (p) REVERT: D 467 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7533 (pt0) REVERT: D 559 ARG cc_start: 0.7134 (mmt90) cc_final: 0.5752 (mtt180) REVERT: D 606 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7601 (mt-10) REVERT: D 673 ASN cc_start: 0.8061 (m-40) cc_final: 0.7355 (t160) REVERT: D 679 ASP cc_start: 0.8629 (t0) cc_final: 0.8400 (t70) REVERT: D 786 ASP cc_start: 0.8723 (p0) cc_final: 0.8450 (p0) REVERT: D 882 GLN cc_start: 0.8636 (mt0) cc_final: 0.8369 (mt0) REVERT: D 898 ASP cc_start: 0.7790 (t0) cc_final: 0.7548 (t0) REVERT: D 1090 MET cc_start: 0.7860 (tmm) cc_final: 0.7496 (tmm) REVERT: D 1170 ASP cc_start: 0.7589 (m-30) cc_final: 0.7222 (m-30) REVERT: D 1244 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.6882 (mp) REVERT: D 1262 ASN cc_start: 0.7191 (p0) cc_final: 0.6830 (p0) REVERT: D 1354 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: E 38 ASN cc_start: 0.6923 (m110) cc_final: 0.6712 (m110) REVERT: E 46 GLU cc_start: 0.8627 (tt0) cc_final: 0.8405 (tt0) REVERT: E 51 ASP cc_start: 0.8030 (t70) cc_final: 0.7749 (m-30) REVERT: E 264 GLU cc_start: 0.8103 (pt0) cc_final: 0.7601 (tt0) REVERT: E 375 ASN cc_start: 0.6893 (t0) cc_final: 0.6619 (t0) REVERT: E 409 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7201 (mt0) REVERT: E 467 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 472 GLN cc_start: 0.6853 (mt0) cc_final: 0.6592 (mm110) REVERT: E 543 THR cc_start: 0.8593 (m) cc_final: 0.8296 (p) REVERT: E 559 ARG cc_start: 0.7437 (mmt90) cc_final: 0.6375 (mtt180) REVERT: E 695 ASP cc_start: 0.7362 (p0) cc_final: 0.6828 (m-30) REVERT: E 765 MET cc_start: 0.8584 (tpp) cc_final: 0.8062 (tpp) REVERT: E 874 ASP cc_start: 0.8217 (m-30) cc_final: 0.7904 (m-30) REVERT: E 898 ASP cc_start: 0.7357 (t0) cc_final: 0.6964 (t70) REVERT: E 987 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7247 (mp0) REVERT: E 999 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: E 1019 ASP cc_start: 0.5983 (t0) cc_final: 0.5412 (t70) REVERT: E 1032 ASP cc_start: 0.6338 (m-30) cc_final: 0.6066 (m-30) REVERT: E 1120 LYS cc_start: 0.7605 (mttt) cc_final: 0.6735 (ttmm) REVERT: E 1262 ASN cc_start: 0.7159 (p0) cc_final: 0.6952 (p0) REVERT: E 1318 GLU cc_start: 0.7181 (tt0) cc_final: 0.6321 (tp30) REVERT: E 1327 LYS cc_start: 0.7885 (mttt) cc_final: 0.7232 (pttt) REVERT: E 1329 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: E 1354 GLU cc_start: 0.7484 (tt0) cc_final: 0.6828 (mt-10) REVERT: F 51 ASP cc_start: 0.8587 (t70) cc_final: 0.8253 (m-30) REVERT: F 54 MET cc_start: 0.8523 (ptm) cc_final: 0.8263 (ptm) REVERT: F 71 ASP cc_start: 0.8502 (p0) cc_final: 0.8141 (m-30) REVERT: F 74 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7288 (mt-10) REVERT: F 116 THR cc_start: 0.7497 (m) cc_final: 0.7075 (p) REVERT: F 472 GLN cc_start: 0.7644 (mt0) cc_final: 0.7168 (mm-40) REVERT: F 499 ASP cc_start: 0.8227 (m-30) cc_final: 0.7893 (m-30) REVERT: F 606 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7384 (tt0) REVERT: F 693 ASN cc_start: 0.7026 (m-40) cc_final: 0.6806 (m110) REVERT: F 885 SER cc_start: 0.8663 (t) cc_final: 0.8363 (p) REVERT: F 1091 ASP cc_start: 0.6683 (m-30) cc_final: 0.6093 (p0) REVERT: F 1138 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6368 (pp20) REVERT: F 1182 LYS cc_start: 0.7545 (mppt) cc_final: 0.7271 (mtmm) REVERT: F 1276 ASP cc_start: 0.7116 (t0) cc_final: 0.6901 (t0) REVERT: F 1318 GLU cc_start: 0.6786 (tt0) cc_final: 0.6380 (tt0) outliers start: 116 outliers final: 33 residues processed: 772 average time/residue: 1.1027 time to fit residues: 1152.6637 Evaluate side-chains 548 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 507 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1244 ILE Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 730 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 999 GLU Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 592 ASP Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 598 optimal weight: 2.9990 chunk 489 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 720 optimal weight: 10.0000 chunk 778 optimal weight: 0.9980 chunk 641 optimal weight: 20.0000 chunk 714 optimal weight: 10.0000 chunk 245 optimal weight: 20.0000 chunk 578 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 663 ASN B 697 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 364 GLN C 623 ASN C1196 GLN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 ASN E 663 ASN E 697 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN F 242 GLN F 364 GLN F 623 ASN F1196 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 60000 Z= 0.302 Angle : 0.617 7.717 82068 Z= 0.340 Chirality : 0.048 0.174 9798 Planarity : 0.004 0.039 11058 Dihedral : 5.304 72.611 8313 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.45 % Allowed : 11.64 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 7950 helix: -2.08 (0.18), residues: 594 sheet: 0.97 (0.11), residues: 2222 loop : -0.81 (0.08), residues: 5134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 297 HIS 0.006 0.001 HIS F 279 PHE 0.024 0.002 PHE D 124 TYR 0.020 0.002 TYR B 972 ARG 0.006 0.001 ARG F1117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 523 time to evaluate : 5.075 Fit side-chains REVERT: A 83 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7843 (t) REVERT: A 320 ASP cc_start: 0.7918 (m-30) cc_final: 0.7663 (m-30) REVERT: A 321 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: A 350 ASP cc_start: 0.7616 (t0) cc_final: 0.7395 (t0) REVERT: A 421 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: A 467 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7660 (pt0) REVERT: A 559 ARG cc_start: 0.7120 (mmt90) cc_final: 0.5746 (mtt180) REVERT: A 606 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8005 (tp30) REVERT: A 610 GLU cc_start: 0.6217 (pt0) cc_final: 0.5970 (mt-10) REVERT: A 673 ASN cc_start: 0.8125 (m-40) cc_final: 0.7417 (t0) REVERT: A 679 ASP cc_start: 0.8695 (t0) cc_final: 0.8476 (t70) REVERT: A 786 ASP cc_start: 0.8789 (p0) cc_final: 0.8543 (p0) REVERT: A 898 ASP cc_start: 0.7961 (t0) cc_final: 0.7718 (t0) REVERT: A 1082 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: A 1150 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: A 1170 ASP cc_start: 0.7633 (m-30) cc_final: 0.7274 (m-30) REVERT: A 1262 ASN cc_start: 0.7564 (p0) cc_final: 0.7164 (t0) REVERT: A 1276 ASP cc_start: 0.6902 (t70) cc_final: 0.6493 (t0) REVERT: A 1354 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: B 46 GLU cc_start: 0.8592 (tt0) cc_final: 0.8352 (tt0) REVERT: B 51 ASP cc_start: 0.8129 (t70) cc_final: 0.7722 (m-30) REVERT: B 83 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 375 ASN cc_start: 0.6891 (t0) cc_final: 0.6488 (t0) REVERT: B 409 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7576 (mt0) REVERT: B 467 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7950 (mt-10) REVERT: B 472 GLN cc_start: 0.7199 (mt0) cc_final: 0.6965 (mm110) REVERT: B 543 THR cc_start: 0.8817 (m) cc_final: 0.8399 (p) REVERT: B 675 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: B 695 ASP cc_start: 0.7026 (p0) cc_final: 0.6660 (m-30) REVERT: B 898 ASP cc_start: 0.7534 (t0) cc_final: 0.7097 (t70) REVERT: B 987 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7290 (mp0) REVERT: B 1165 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6285 (mp10) REVERT: B 1318 GLU cc_start: 0.7268 (tt0) cc_final: 0.6522 (tp30) REVERT: B 1327 LYS cc_start: 0.7810 (mttt) cc_final: 0.7191 (pttt) REVERT: B 1354 GLU cc_start: 0.7554 (tt0) cc_final: 0.6826 (mt-10) REVERT: C 46 GLU cc_start: 0.8258 (tt0) cc_final: 0.7924 (tp30) REVERT: C 51 ASP cc_start: 0.8683 (t70) cc_final: 0.8316 (m-30) REVERT: C 71 ASP cc_start: 0.8695 (p0) cc_final: 0.8236 (m-30) REVERT: C 116 THR cc_start: 0.7806 (m) cc_final: 0.7295 (p) REVERT: C 472 GLN cc_start: 0.7748 (mt0) cc_final: 0.7086 (mm-40) REVERT: C 606 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7332 (tt0) REVERT: C 797 ASP cc_start: 0.8487 (t70) cc_final: 0.8234 (t70) REVERT: C 885 SER cc_start: 0.8643 (t) cc_final: 0.8377 (p) REVERT: C 978 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: C 1090 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6591 (ttp) REVERT: C 1091 ASP cc_start: 0.6758 (m-30) cc_final: 0.6412 (p0) REVERT: C 1138 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6408 (pp20) REVERT: C 1233 ASN cc_start: 0.6190 (p0) cc_final: 0.5982 (m110) REVERT: C 1240 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5577 (pttt) REVERT: D 83 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7812 (t) REVERT: D 321 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6370 (pm20) REVERT: D 350 ASP cc_start: 0.7619 (t0) cc_final: 0.7399 (t0) REVERT: D 467 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7659 (pt0) REVERT: D 559 ARG cc_start: 0.7120 (mmt90) cc_final: 0.5748 (mtt180) REVERT: D 606 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8054 (tp30) REVERT: D 673 ASN cc_start: 0.8126 (m-40) cc_final: 0.7414 (t0) REVERT: D 679 ASP cc_start: 0.8661 (t0) cc_final: 0.8440 (t70) REVERT: D 786 ASP cc_start: 0.8792 (p0) cc_final: 0.8546 (p0) REVERT: D 898 ASP cc_start: 0.7960 (t0) cc_final: 0.7717 (t0) REVERT: D 1082 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: D 1090 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7717 (tmm) REVERT: D 1150 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: D 1170 ASP cc_start: 0.7634 (m-30) cc_final: 0.7259 (m-30) REVERT: D 1262 ASN cc_start: 0.7560 (p0) cc_final: 0.7161 (t0) REVERT: D 1276 ASP cc_start: 0.6875 (t70) cc_final: 0.6482 (t0) REVERT: D 1354 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7039 (tt0) REVERT: E 46 GLU cc_start: 0.8635 (tt0) cc_final: 0.8392 (tt0) REVERT: E 51 ASP cc_start: 0.8133 (t70) cc_final: 0.7724 (m-30) REVERT: E 83 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7721 (m) REVERT: E 375 ASN cc_start: 0.6904 (t0) cc_final: 0.6522 (t0) REVERT: E 409 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7578 (mt0) REVERT: E 467 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8046 (mt-10) REVERT: E 543 THR cc_start: 0.8819 (m) cc_final: 0.8403 (p) REVERT: E 675 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: E 695 ASP cc_start: 0.6962 (p0) cc_final: 0.6651 (m-30) REVERT: E 898 ASP cc_start: 0.7532 (t0) cc_final: 0.7096 (t70) REVERT: E 987 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7292 (mp0) REVERT: E 999 GLU cc_start: 0.7006 (mp0) cc_final: 0.6543 (mp0) REVERT: E 1165 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6286 (mp10) REVERT: E 1318 GLU cc_start: 0.7264 (tt0) cc_final: 0.6519 (tp30) REVERT: E 1327 LYS cc_start: 0.7899 (mttt) cc_final: 0.7300 (pttt) REVERT: E 1354 GLU cc_start: 0.7552 (tt0) cc_final: 0.6825 (mt-10) REVERT: F 46 GLU cc_start: 0.8352 (tt0) cc_final: 0.7949 (tp30) REVERT: F 51 ASP cc_start: 0.8683 (t70) cc_final: 0.8318 (m-30) REVERT: F 54 MET cc_start: 0.8523 (ptm) cc_final: 0.8306 (ptm) REVERT: F 71 ASP cc_start: 0.8720 (p0) cc_final: 0.8244 (m-30) REVERT: F 116 THR cc_start: 0.7799 (m) cc_final: 0.7290 (p) REVERT: F 472 GLN cc_start: 0.7751 (mt0) cc_final: 0.7088 (mm-40) REVERT: F 606 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7333 (tt0) REVERT: F 797 ASP cc_start: 0.8485 (t70) cc_final: 0.8231 (t70) REVERT: F 885 SER cc_start: 0.8652 (t) cc_final: 0.8377 (p) REVERT: F 978 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: F 1090 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6583 (ttp) REVERT: F 1091 ASP cc_start: 0.6750 (m-30) cc_final: 0.6406 (p0) REVERT: F 1138 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6396 (pp20) REVERT: F 1233 ASN cc_start: 0.6197 (p0) cc_final: 0.5977 (m110) outliers start: 162 outliers final: 82 residues processed: 657 average time/residue: 1.0715 time to fit residues: 967.5217 Evaluate side-chains 586 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 481 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1082 GLU Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1104 SER Chi-restraints excluded: chain B residue 1165 GLN Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1240 LYS Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 750 THR Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1104 SER Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 911 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1153 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 7.9990 chunk 541 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 chunk 483 optimal weight: 20.0000 chunk 723 optimal weight: 0.8980 chunk 765 optimal weight: 20.0000 chunk 377 optimal weight: 10.0000 chunk 685 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN D 583 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 697 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 60000 Z= 0.224 Angle : 0.550 6.870 82068 Z= 0.302 Chirality : 0.046 0.158 9798 Planarity : 0.004 0.044 11058 Dihedral : 5.032 66.556 8310 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.88 % Allowed : 12.00 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.09), residues: 7950 helix: -2.04 (0.19), residues: 594 sheet: 0.96 (0.11), residues: 2196 loop : -0.77 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1275 HIS 0.004 0.001 HIS F 279 PHE 0.017 0.002 PHE D 102 TYR 0.018 0.002 TYR F1268 ARG 0.004 0.000 ARG C1117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 496 time to evaluate : 4.972 Fit side-chains REVERT: A 83 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7839 (t) REVERT: A 320 ASP cc_start: 0.7893 (m-30) cc_final: 0.7637 (m-30) REVERT: A 321 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: A 350 ASP cc_start: 0.7615 (t0) cc_final: 0.7384 (t0) REVERT: A 421 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: A 467 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7633 (pt0) REVERT: A 559 ARG cc_start: 0.7119 (mmt90) cc_final: 0.5728 (mtt180) REVERT: A 606 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7982 (tp30) REVERT: A 610 GLU cc_start: 0.6347 (pt0) cc_final: 0.6053 (mt-10) REVERT: A 673 ASN cc_start: 0.8206 (m-40) cc_final: 0.7516 (t0) REVERT: A 679 ASP cc_start: 0.8718 (t0) cc_final: 0.8491 (t70) REVERT: A 786 ASP cc_start: 0.8805 (p0) cc_final: 0.8565 (p0) REVERT: A 898 ASP cc_start: 0.7921 (t0) cc_final: 0.7679 (t0) REVERT: A 1090 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7052 (mmm) REVERT: A 1150 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: A 1170 ASP cc_start: 0.7572 (m-30) cc_final: 0.7200 (m-30) REVERT: A 1276 ASP cc_start: 0.7051 (t70) cc_final: 0.6581 (t0) REVERT: A 1330 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6729 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: B 46 GLU cc_start: 0.8637 (tt0) cc_final: 0.8384 (tt0) REVERT: B 51 ASP cc_start: 0.8183 (t70) cc_final: 0.7817 (m-30) REVERT: B 83 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7702 (m) REVERT: B 264 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: B 409 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7582 (mt0) REVERT: B 467 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7946 (mt-10) REVERT: B 472 GLN cc_start: 0.7214 (mt0) cc_final: 0.6962 (mm110) REVERT: B 543 THR cc_start: 0.8840 (m) cc_final: 0.8422 (p) REVERT: B 675 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: B 891 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7681 (tmm-80) REVERT: B 987 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7287 (mp0) REVERT: B 1165 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6211 (mp10) REVERT: B 1302 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: B 1318 GLU cc_start: 0.7277 (tt0) cc_final: 0.6567 (tp30) REVERT: B 1327 LYS cc_start: 0.7976 (mttt) cc_final: 0.7341 (pttt) REVERT: B 1354 GLU cc_start: 0.7488 (tt0) cc_final: 0.6749 (mt-10) REVERT: C 46 GLU cc_start: 0.8270 (tt0) cc_final: 0.7951 (tp30) REVERT: C 51 ASP cc_start: 0.8632 (t70) cc_final: 0.8314 (m-30) REVERT: C 116 THR cc_start: 0.7864 (m) cc_final: 0.7406 (p) REVERT: C 269 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.5958 (mtp180) REVERT: C 606 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7336 (tt0) REVERT: C 797 ASP cc_start: 0.8440 (t70) cc_final: 0.8162 (t70) REVERT: C 885 SER cc_start: 0.8669 (t) cc_final: 0.8391 (p) REVERT: C 978 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: C 1090 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6544 (ttp) REVERT: C 1091 ASP cc_start: 0.6725 (m-30) cc_final: 0.6400 (p0) REVERT: C 1101 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6641 (pp) REVERT: C 1138 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6410 (pp20) REVERT: C 1240 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.5597 (pttt) REVERT: D 83 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7834 (t) REVERT: D 321 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6037 (pm20) REVERT: D 350 ASP cc_start: 0.7617 (t0) cc_final: 0.7388 (t0) REVERT: D 467 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7629 (pt0) REVERT: D 559 ARG cc_start: 0.7118 (mmt90) cc_final: 0.5742 (mtt180) REVERT: D 606 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8069 (tp30) REVERT: D 673 ASN cc_start: 0.8208 (m-40) cc_final: 0.7515 (t0) REVERT: D 679 ASP cc_start: 0.8656 (t0) cc_final: 0.8435 (t70) REVERT: D 786 ASP cc_start: 0.8808 (p0) cc_final: 0.8572 (p0) REVERT: D 898 ASP cc_start: 0.7919 (t0) cc_final: 0.7674 (t0) REVERT: D 1082 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: D 1090 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7644 (tmm) REVERT: D 1150 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: D 1170 ASP cc_start: 0.7575 (m-30) cc_final: 0.7204 (m-30) REVERT: D 1276 ASP cc_start: 0.7087 (t70) cc_final: 0.6636 (t0) REVERT: D 1354 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: E 46 GLU cc_start: 0.8642 (tt0) cc_final: 0.8389 (tt0) REVERT: E 51 ASP cc_start: 0.8185 (t70) cc_final: 0.7818 (m-30) REVERT: E 83 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7704 (m) REVERT: E 264 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: E 409 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7584 (mt0) REVERT: E 467 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 472 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7319 (mm110) REVERT: E 473 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: E 543 THR cc_start: 0.8842 (m) cc_final: 0.8423 (p) REVERT: E 675 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: E 891 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7677 (tmm-80) REVERT: E 898 ASP cc_start: 0.7488 (t0) cc_final: 0.7023 (t70) REVERT: E 987 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7290 (mp0) REVERT: E 999 GLU cc_start: 0.7126 (mp0) cc_final: 0.6851 (mp0) REVERT: E 1165 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6213 (mp10) REVERT: E 1302 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: E 1318 GLU cc_start: 0.7277 (tt0) cc_final: 0.6554 (tp30) REVERT: E 1327 LYS cc_start: 0.7968 (mttt) cc_final: 0.7319 (pttt) REVERT: E 1354 GLU cc_start: 0.7492 (tt0) cc_final: 0.6757 (mt-10) REVERT: F 46 GLU cc_start: 0.8382 (tt0) cc_final: 0.7973 (tp30) REVERT: F 51 ASP cc_start: 0.8649 (t70) cc_final: 0.8314 (m-30) REVERT: F 116 THR cc_start: 0.7857 (m) cc_final: 0.7400 (p) REVERT: F 269 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.5911 (mtp180) REVERT: F 606 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7338 (tt0) REVERT: F 797 ASP cc_start: 0.8443 (t70) cc_final: 0.8163 (t70) REVERT: F 885 SER cc_start: 0.8676 (t) cc_final: 0.8388 (p) REVERT: F 978 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: F 1091 ASP cc_start: 0.6723 (m-30) cc_final: 0.6397 (p0) REVERT: F 1101 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6643 (pp) REVERT: F 1138 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6417 (pp20) outliers start: 190 outliers final: 87 residues processed: 645 average time/residue: 1.0908 time to fit residues: 963.5502 Evaluate side-chains 572 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 450 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1165 GLN Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1240 LYS Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 10.0000 chunk 434 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 570 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 653 optimal weight: 20.0000 chunk 529 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 390 optimal weight: 20.0000 chunk 687 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 583 GLN A 623 ASN A 693 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 ASN B 697 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 GLN D 623 ASN D 693 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 583 GLN E 623 ASN E 697 ASN ** E 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 60000 Z= 0.337 Angle : 0.625 7.943 82068 Z= 0.344 Chirality : 0.049 0.169 9798 Planarity : 0.004 0.047 11058 Dihedral : 5.364 63.413 8310 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.67 % Allowed : 11.79 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.09), residues: 7950 helix: -1.99 (0.19), residues: 566 sheet: 0.80 (0.11), residues: 2210 loop : -0.82 (0.08), residues: 5174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 297 HIS 0.005 0.001 HIS F 279 PHE 0.022 0.002 PHE A 102 TYR 0.020 0.002 TYR D 972 ARG 0.005 0.001 ARG C1117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 471 time to evaluate : 5.103 Fit side-chains REVERT: A 83 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7898 (t) REVERT: A 321 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: A 350 ASP cc_start: 0.7657 (t0) cc_final: 0.7406 (t0) REVERT: A 421 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: A 467 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7657 (pt0) REVERT: A 559 ARG cc_start: 0.7100 (mmt90) cc_final: 0.5696 (mtt180) REVERT: A 606 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7955 (tp30) REVERT: A 610 GLU cc_start: 0.6381 (pt0) cc_final: 0.6079 (mt-10) REVERT: A 657 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6838 (ttt90) REVERT: A 673 ASN cc_start: 0.8240 (m-40) cc_final: 0.7550 (t0) REVERT: A 737 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7992 (mtt-85) REVERT: A 786 ASP cc_start: 0.8902 (p0) cc_final: 0.8681 (p0) REVERT: A 1090 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7055 (mmm) REVERT: A 1150 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: A 1170 ASP cc_start: 0.7621 (m-30) cc_final: 0.7263 (m-30) REVERT: A 1276 ASP cc_start: 0.7138 (t70) cc_final: 0.6581 (t0) REVERT: A 1330 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6507 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: B 46 GLU cc_start: 0.8628 (tt0) cc_final: 0.8390 (tt0) REVERT: B 51 ASP cc_start: 0.8288 (t70) cc_final: 0.7895 (m-30) REVERT: B 68 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: B 83 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 264 GLU cc_start: 0.8206 (pt0) cc_final: 0.7401 (tt0) REVERT: B 409 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7608 (mt0) REVERT: B 467 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 543 THR cc_start: 0.8819 (m) cc_final: 0.8403 (p) REVERT: B 567 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 675 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: B 855 ASP cc_start: 0.7611 (t70) cc_final: 0.7380 (t70) REVERT: B 891 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7771 (tmm-80) REVERT: B 987 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7360 (mp0) REVERT: B 1165 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: B 1190 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6305 (t70) REVERT: B 1302 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: B 1318 GLU cc_start: 0.7301 (tt0) cc_final: 0.6573 (tp30) REVERT: B 1327 LYS cc_start: 0.7888 (mttt) cc_final: 0.7268 (pttt) REVERT: B 1354 GLU cc_start: 0.7503 (tt0) cc_final: 0.6866 (mm-30) REVERT: B 1363 SER cc_start: 0.6060 (OUTLIER) cc_final: 0.5826 (t) REVERT: C 46 GLU cc_start: 0.8274 (tt0) cc_final: 0.7941 (tp30) REVERT: C 51 ASP cc_start: 0.8617 (t70) cc_final: 0.8308 (m-30) REVERT: C 71 ASP cc_start: 0.8821 (p0) cc_final: 0.8528 (m-30) REVERT: C 116 THR cc_start: 0.8168 (m) cc_final: 0.7587 (p) REVERT: C 606 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7333 (tt0) REVERT: C 797 ASP cc_start: 0.8452 (t70) cc_final: 0.8148 (t70) REVERT: C 885 SER cc_start: 0.8661 (t) cc_final: 0.8374 (p) REVERT: C 978 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 1090 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6501 (ttp) REVERT: C 1091 ASP cc_start: 0.6756 (m-30) cc_final: 0.6403 (p0) REVERT: C 1101 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6779 (pp) REVERT: C 1138 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6395 (pp20) REVERT: C 1150 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: C 1323 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6872 (mm) REVERT: D 83 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7897 (t) REVERT: D 321 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5926 (pm20) REVERT: D 350 ASP cc_start: 0.7661 (t0) cc_final: 0.7409 (t0) REVERT: D 467 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7660 (pt0) REVERT: D 559 ARG cc_start: 0.7115 (mmt90) cc_final: 0.5691 (mtt180) REVERT: D 606 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8085 (tp30) REVERT: D 657 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6858 (ttt90) REVERT: D 673 ASN cc_start: 0.8241 (m-40) cc_final: 0.7550 (t0) REVERT: D 679 ASP cc_start: 0.8651 (t0) cc_final: 0.8429 (t70) REVERT: D 786 ASP cc_start: 0.8905 (p0) cc_final: 0.8676 (p0) REVERT: D 1082 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: D 1090 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (tmm) REVERT: D 1150 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: D 1170 ASP cc_start: 0.7622 (m-30) cc_final: 0.7266 (m-30) REVERT: D 1276 ASP cc_start: 0.7181 (t70) cc_final: 0.6636 (t0) REVERT: D 1354 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: E 46 GLU cc_start: 0.8642 (tt0) cc_final: 0.8394 (tt0) REVERT: E 51 ASP cc_start: 0.8291 (t70) cc_final: 0.7905 (m-30) REVERT: E 83 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7742 (m) REVERT: E 264 GLU cc_start: 0.8205 (pt0) cc_final: 0.7399 (tt0) REVERT: E 409 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7610 (mt0) REVERT: E 467 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7939 (mt-10) REVERT: E 472 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7388 (mm110) REVERT: E 473 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: E 543 THR cc_start: 0.8821 (m) cc_final: 0.8406 (p) REVERT: E 567 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (t) REVERT: E 583 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: E 675 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: E 855 ASP cc_start: 0.7612 (t70) cc_final: 0.7382 (t70) REVERT: E 891 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7770 (tmm-80) REVERT: E 898 ASP cc_start: 0.7429 (t0) cc_final: 0.6961 (t70) REVERT: E 987 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7364 (mp0) REVERT: E 999 GLU cc_start: 0.7177 (mp0) cc_final: 0.6914 (mp0) REVERT: E 1165 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6244 (mp10) REVERT: E 1190 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6271 (t70) REVERT: E 1302 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: E 1318 GLU cc_start: 0.7300 (tt0) cc_final: 0.6564 (tp30) REVERT: E 1327 LYS cc_start: 0.7964 (mttt) cc_final: 0.7326 (pttt) REVERT: E 1329 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: E 1354 GLU cc_start: 0.7455 (tt0) cc_final: 0.6805 (mm-30) REVERT: E 1363 SER cc_start: 0.6047 (OUTLIER) cc_final: 0.5812 (t) REVERT: F 46 GLU cc_start: 0.8350 (tt0) cc_final: 0.7920 (tp30) REVERT: F 51 ASP cc_start: 0.8617 (t70) cc_final: 0.8309 (m-30) REVERT: F 71 ASP cc_start: 0.8840 (p0) cc_final: 0.8537 (m-30) REVERT: F 116 THR cc_start: 0.8163 (m) cc_final: 0.7582 (p) REVERT: F 606 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7332 (tt0) REVERT: F 797 ASP cc_start: 0.8451 (t70) cc_final: 0.8148 (t70) REVERT: F 885 SER cc_start: 0.8670 (t) cc_final: 0.8370 (p) REVERT: F 978 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: F 1090 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6506 (ttp) REVERT: F 1091 ASP cc_start: 0.6765 (m-30) cc_final: 0.6415 (p0) REVERT: F 1101 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6776 (pp) REVERT: F 1138 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6389 (pp20) REVERT: F 1150 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7189 (tt0) outliers start: 242 outliers final: 126 residues processed: 660 average time/residue: 1.1112 time to fit residues: 992.0994 Evaluate side-chains 601 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 429 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1165 GLN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1336 LEU Chi-restraints excluded: chain B residue 1363 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1323 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 531 ASP Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 583 GLN Chi-restraints excluded: chain D residue 657 ARG Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1315 ILE Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 583 GLN Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 750 THR Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1190 ASP Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1336 LEU Chi-restraints excluded: chain E residue 1363 SER Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 911 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 0.8980 chunk 689 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 449 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 766 optimal weight: 20.0000 chunk 636 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 253 optimal weight: 20.0000 chunk 402 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A1167 ASN B 38 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 583 GLN B 697 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN C1196 GLN C1262 ASN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D1167 ASN E 38 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN E 697 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 ASN F1196 GLN F1262 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 60000 Z= 0.316 Angle : 0.608 7.600 82068 Z= 0.334 Chirality : 0.048 0.166 9798 Planarity : 0.004 0.050 11058 Dihedral : 5.307 60.165 8308 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.50 % Allowed : 12.15 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.09), residues: 7950 helix: -2.03 (0.18), residues: 566 sheet: 0.77 (0.11), residues: 2216 loop : -0.85 (0.08), residues: 5168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1275 HIS 0.005 0.001 HIS F 279 PHE 0.023 0.002 PHE A 102 TYR 0.017 0.002 TYR B 972 ARG 0.005 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 457 time to evaluate : 4.942 Fit side-chains REVERT: A 83 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7868 (t) REVERT: A 321 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: A 350 ASP cc_start: 0.7657 (t0) cc_final: 0.7400 (t0) REVERT: A 421 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 467 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7663 (pt0) REVERT: A 559 ARG cc_start: 0.7112 (mmt90) cc_final: 0.5691 (mtt180) REVERT: A 606 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7972 (tp30) REVERT: A 610 GLU cc_start: 0.6412 (pt0) cc_final: 0.6115 (mt-10) REVERT: A 657 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6861 (ttt90) REVERT: A 673 ASN cc_start: 0.8178 (m-40) cc_final: 0.7541 (t160) REVERT: A 721 ASP cc_start: 0.8538 (m-30) cc_final: 0.8265 (m-30) REVERT: A 737 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8045 (mtt-85) REVERT: A 786 ASP cc_start: 0.8894 (p0) cc_final: 0.8680 (p0) REVERT: A 1090 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7039 (mmm) REVERT: A 1150 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: A 1170 ASP cc_start: 0.7600 (m-30) cc_final: 0.7232 (m-30) REVERT: A 1276 ASP cc_start: 0.7101 (t70) cc_final: 0.6555 (t0) REVERT: A 1330 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6577 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: B 46 GLU cc_start: 0.8645 (tt0) cc_final: 0.8392 (tt0) REVERT: B 51 ASP cc_start: 0.8286 (t70) cc_final: 0.7929 (m-30) REVERT: B 68 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: B 83 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7728 (m) REVERT: B 264 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 409 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7617 (mt0) REVERT: B 467 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 543 THR cc_start: 0.8833 (m) cc_final: 0.8412 (p) REVERT: B 567 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8223 (t) REVERT: B 583 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: B 675 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: B 855 ASP cc_start: 0.7610 (t70) cc_final: 0.7370 (t70) REVERT: B 891 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7726 (tmm-80) REVERT: B 987 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7363 (mp0) REVERT: B 1165 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6284 (mp10) REVERT: B 1190 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6298 (t70) REVERT: B 1302 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: B 1318 GLU cc_start: 0.7317 (tt0) cc_final: 0.6590 (tp30) REVERT: B 1327 LYS cc_start: 0.7887 (mttt) cc_final: 0.7261 (pttt) REVERT: B 1352 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5710 (tt0) REVERT: B 1354 GLU cc_start: 0.7380 (tt0) cc_final: 0.6766 (mm-30) REVERT: B 1363 SER cc_start: 0.6043 (OUTLIER) cc_final: 0.5839 (t) REVERT: C 46 GLU cc_start: 0.8322 (tt0) cc_final: 0.7996 (tp30) REVERT: C 51 ASP cc_start: 0.8615 (t70) cc_final: 0.8307 (m-30) REVERT: C 116 THR cc_start: 0.8157 (m) cc_final: 0.7576 (p) REVERT: C 606 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7439 (tt0) REVERT: C 797 ASP cc_start: 0.8402 (t70) cc_final: 0.8129 (t70) REVERT: C 885 SER cc_start: 0.8685 (t) cc_final: 0.8387 (p) REVERT: C 978 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 1090 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6545 (ttp) REVERT: C 1091 ASP cc_start: 0.6753 (m-30) cc_final: 0.6458 (p0) REVERT: C 1101 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6797 (pp) REVERT: C 1138 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6353 (pp20) REVERT: C 1150 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: C 1323 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6911 (mm) REVERT: C 1359 THR cc_start: 0.8093 (t) cc_final: 0.7662 (m) REVERT: D 83 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7873 (t) REVERT: D 321 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5923 (pm20) REVERT: D 350 ASP cc_start: 0.7659 (t0) cc_final: 0.7402 (t0) REVERT: D 467 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7664 (pt0) REVERT: D 559 ARG cc_start: 0.7110 (mmt90) cc_final: 0.5691 (mtt180) REVERT: D 606 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8079 (tp30) REVERT: D 657 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6872 (ttt90) REVERT: D 673 ASN cc_start: 0.8168 (m-40) cc_final: 0.7525 (t160) REVERT: D 679 ASP cc_start: 0.8654 (t0) cc_final: 0.8431 (t70) REVERT: D 721 ASP cc_start: 0.8432 (m-30) cc_final: 0.8160 (m-30) REVERT: D 737 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8003 (mtt-85) REVERT: D 786 ASP cc_start: 0.8896 (p0) cc_final: 0.8681 (p0) REVERT: D 1082 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: D 1090 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7540 (tmm) REVERT: D 1150 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: D 1170 ASP cc_start: 0.7606 (m-30) cc_final: 0.7239 (m-30) REVERT: D 1276 ASP cc_start: 0.7123 (t70) cc_final: 0.6563 (t0) REVERT: D 1354 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: E 46 GLU cc_start: 0.8651 (tt0) cc_final: 0.8399 (tt0) REVERT: E 51 ASP cc_start: 0.8288 (t70) cc_final: 0.7929 (m-30) REVERT: E 83 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7732 (m) REVERT: E 264 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: E 409 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7619 (mt0) REVERT: E 467 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7950 (mt-10) REVERT: E 472 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: E 473 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: E 543 THR cc_start: 0.8834 (m) cc_final: 0.8412 (p) REVERT: E 567 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8162 (t) REVERT: E 583 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: E 675 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: E 855 ASP cc_start: 0.7619 (t70) cc_final: 0.7379 (t70) REVERT: E 891 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7723 (tmm-80) REVERT: E 987 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7364 (mp0) REVERT: E 999 GLU cc_start: 0.7199 (mp0) cc_final: 0.6945 (mp0) REVERT: E 1165 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6286 (mp10) REVERT: E 1190 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6295 (t70) REVERT: E 1302 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: E 1318 GLU cc_start: 0.7312 (tt0) cc_final: 0.6587 (tp30) REVERT: E 1327 LYS cc_start: 0.7952 (mttt) cc_final: 0.7329 (pttt) REVERT: E 1329 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: E 1352 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5669 (tt0) REVERT: E 1354 GLU cc_start: 0.7375 (tt0) cc_final: 0.6664 (mt-10) REVERT: E 1363 SER cc_start: 0.6035 (OUTLIER) cc_final: 0.5830 (t) REVERT: F 46 GLU cc_start: 0.8383 (tt0) cc_final: 0.7963 (tp30) REVERT: F 51 ASP cc_start: 0.8618 (t70) cc_final: 0.8314 (m-30) REVERT: F 116 THR cc_start: 0.8154 (m) cc_final: 0.7574 (p) REVERT: F 606 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7437 (tt0) REVERT: F 797 ASP cc_start: 0.8402 (t70) cc_final: 0.8129 (t70) REVERT: F 885 SER cc_start: 0.8693 (t) cc_final: 0.8383 (p) REVERT: F 978 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: F 1063 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: F 1090 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6487 (ttp) REVERT: F 1091 ASP cc_start: 0.6759 (m-30) cc_final: 0.6464 (p0) REVERT: F 1101 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6797 (pp) REVERT: F 1138 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6379 (pp20) REVERT: F 1150 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: F 1359 THR cc_start: 0.8094 (t) cc_final: 0.7660 (m) outliers start: 231 outliers final: 135 residues processed: 642 average time/residue: 1.0695 time to fit residues: 937.6042 Evaluate side-chains 619 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 431 time to evaluate : 4.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 583 GLN Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1165 GLN Chi-restraints excluded: chain B residue 1190 ASP Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1336 LEU Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1363 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1056 SER Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1262 ASN Chi-restraints excluded: chain C residue 1323 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 657 ARG Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 737 ARG Chi-restraints excluded: chain D residue 822 GLU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1201 LEU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 583 GLN Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1190 ASP Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1363 SER Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 525 THR Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 911 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1056 SER Chi-restraints excluded: chain F residue 1063 GLU Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1262 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 436 optimal weight: 0.5980 chunk 559 optimal weight: 10.0000 chunk 433 optimal weight: 8.9990 chunk 645 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 763 optimal weight: 5.9990 chunk 477 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A1167 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1262 ASN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1167 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN E1233 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1262 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 60000 Z= 0.221 Angle : 0.542 6.688 82068 Z= 0.298 Chirality : 0.046 0.156 9798 Planarity : 0.004 0.051 11058 Dihedral : 4.996 59.926 8308 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.08 % Allowed : 12.86 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.09), residues: 7950 helix: -1.93 (0.18), residues: 594 sheet: 0.90 (0.11), residues: 2160 loop : -0.81 (0.08), residues: 5196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1275 HIS 0.003 0.001 HIS C 279 PHE 0.021 0.001 PHE A 102 TYR 0.015 0.002 TYR F1348 ARG 0.003 0.000 ARG F1134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 458 time to evaluate : 4.995 Fit side-chains REVERT: A 83 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7826 (t) REVERT: A 321 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6000 (pm20) REVERT: A 350 ASP cc_start: 0.7602 (t0) cc_final: 0.7360 (t0) REVERT: A 421 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: A 467 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7650 (pt0) REVERT: A 559 ARG cc_start: 0.7112 (mmt90) cc_final: 0.5701 (mtt180) REVERT: A 606 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8086 (tp30) REVERT: A 673 ASN cc_start: 0.8146 (m-40) cc_final: 0.7513 (t160) REVERT: A 721 ASP cc_start: 0.8418 (m-30) cc_final: 0.8198 (m-30) REVERT: A 786 ASP cc_start: 0.8885 (p0) cc_final: 0.8671 (p0) REVERT: A 1150 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: A 1170 ASP cc_start: 0.7628 (m-30) cc_final: 0.7282 (m-30) REVERT: A 1276 ASP cc_start: 0.7094 (t70) cc_final: 0.6541 (t0) REVERT: A 1330 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6571 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: B 46 GLU cc_start: 0.8645 (tt0) cc_final: 0.8383 (tt0) REVERT: B 51 ASP cc_start: 0.8188 (t70) cc_final: 0.7844 (m-30) REVERT: B 83 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7692 (m) REVERT: B 264 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: B 409 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7605 (mt0) REVERT: B 467 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 472 GLN cc_start: 0.7772 (mm110) cc_final: 0.7526 (mm110) REVERT: B 543 THR cc_start: 0.8833 (m) cc_final: 0.8420 (p) REVERT: B 567 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 583 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: B 675 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 855 ASP cc_start: 0.7595 (t70) cc_final: 0.7353 (t70) REVERT: B 891 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7803 (tmm-80) REVERT: B 987 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7345 (mp0) REVERT: B 1302 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: B 1318 GLU cc_start: 0.7317 (tt0) cc_final: 0.6598 (tp30) REVERT: B 1327 LYS cc_start: 0.7881 (mttt) cc_final: 0.7255 (pttt) REVERT: B 1352 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5751 (tt0) REVERT: B 1354 GLU cc_start: 0.7506 (tt0) cc_final: 0.6757 (mm-30) REVERT: C 46 GLU cc_start: 0.8297 (tt0) cc_final: 0.7977 (tp30) REVERT: C 51 ASP cc_start: 0.8629 (t70) cc_final: 0.8315 (m-30) REVERT: C 116 THR cc_start: 0.8030 (m) cc_final: 0.7467 (p) REVERT: C 232 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: C 606 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7426 (tt0) REVERT: C 885 SER cc_start: 0.8695 (t) cc_final: 0.8377 (p) REVERT: C 978 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: C 1090 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6538 (ttp) REVERT: C 1091 ASP cc_start: 0.6725 (m-30) cc_final: 0.6470 (p0) REVERT: C 1101 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6788 (pp) REVERT: C 1138 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6365 (pp20) REVERT: C 1150 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: C 1323 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6913 (mm) REVERT: C 1359 THR cc_start: 0.7949 (t) cc_final: 0.7516 (m) REVERT: D 83 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7832 (t) REVERT: D 321 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5989 (pm20) REVERT: D 350 ASP cc_start: 0.7605 (t0) cc_final: 0.7363 (t0) REVERT: D 467 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7651 (pt0) REVERT: D 559 ARG cc_start: 0.7113 (mmt90) cc_final: 0.5702 (mtt180) REVERT: D 606 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8039 (tp30) REVERT: D 673 ASN cc_start: 0.8148 (m-40) cc_final: 0.7516 (t160) REVERT: D 679 ASP cc_start: 0.8661 (t0) cc_final: 0.8435 (t70) REVERT: D 721 ASP cc_start: 0.8394 (m-30) cc_final: 0.8157 (m-30) REVERT: D 737 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7918 (mtt-85) REVERT: D 786 ASP cc_start: 0.8888 (p0) cc_final: 0.8674 (p0) REVERT: D 1082 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: D 1090 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7603 (tmm) REVERT: D 1150 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: D 1170 ASP cc_start: 0.7631 (m-30) cc_final: 0.7284 (m-30) REVERT: D 1276 ASP cc_start: 0.7082 (t70) cc_final: 0.6531 (t0) REVERT: D 1354 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: E 46 GLU cc_start: 0.8651 (tt0) cc_final: 0.8389 (tt0) REVERT: E 51 ASP cc_start: 0.8192 (t70) cc_final: 0.7846 (m-30) REVERT: E 83 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7695 (m) REVERT: E 264 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: E 409 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7607 (mt0) REVERT: E 467 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7926 (mt-10) REVERT: E 472 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7427 (mm110) REVERT: E 473 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: E 543 THR cc_start: 0.8833 (m) cc_final: 0.8422 (p) REVERT: E 567 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8115 (t) REVERT: E 583 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: E 675 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: E 891 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7802 (tmm-80) REVERT: E 898 ASP cc_start: 0.7397 (t0) cc_final: 0.6931 (t70) REVERT: E 987 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7348 (mp0) REVERT: E 999 GLU cc_start: 0.7135 (mp0) cc_final: 0.6928 (mp0) REVERT: E 1249 MET cc_start: 0.8300 (ptm) cc_final: 0.7814 (tmm) REVERT: E 1302 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: E 1318 GLU cc_start: 0.7315 (tt0) cc_final: 0.6598 (tp30) REVERT: E 1327 LYS cc_start: 0.7938 (mttt) cc_final: 0.7305 (pttt) REVERT: E 1352 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5724 (tt0) REVERT: E 1354 GLU cc_start: 0.7421 (tt0) cc_final: 0.6803 (mm-30) REVERT: F 46 GLU cc_start: 0.8375 (tt0) cc_final: 0.7952 (tp30) REVERT: F 51 ASP cc_start: 0.8631 (t70) cc_final: 0.8321 (m-30) REVERT: F 116 THR cc_start: 0.8025 (m) cc_final: 0.7462 (p) REVERT: F 606 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7425 (tt0) REVERT: F 841 ASP cc_start: 0.8694 (m-30) cc_final: 0.8487 (m-30) REVERT: F 885 SER cc_start: 0.8701 (t) cc_final: 0.8375 (p) REVERT: F 978 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: F 1063 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: F 1090 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6462 (ttp) REVERT: F 1091 ASP cc_start: 0.6757 (m-30) cc_final: 0.6442 (p0) REVERT: F 1101 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6784 (pp) REVERT: F 1138 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6335 (pp20) REVERT: F 1150 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: F 1323 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6763 (mm) REVERT: F 1359 THR cc_start: 0.7950 (t) cc_final: 0.7515 (m) outliers start: 203 outliers final: 123 residues processed: 625 average time/residue: 1.0949 time to fit residues: 932.1332 Evaluate side-chains 592 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 426 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 583 GLN Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1209 GLU Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1056 SER Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1323 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 737 ARG Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1082 GLU Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 583 GLN Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1209 GLU Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1233 ASN Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 525 THR Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1056 SER Chi-restraints excluded: chain F residue 1063 GLU Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 4.9990 chunk 304 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 485 optimal weight: 1.9990 chunk 520 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 600 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A1167 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1167 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN ** E 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 60000 Z= 0.326 Angle : 0.614 7.676 82068 Z= 0.338 Chirality : 0.049 0.167 9798 Planarity : 0.004 0.052 11058 Dihedral : 5.288 61.310 8308 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.20 % Allowed : 13.06 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.09), residues: 7950 helix: -2.06 (0.18), residues: 594 sheet: 0.76 (0.11), residues: 2212 loop : -0.85 (0.08), residues: 5144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1275 HIS 0.005 0.001 HIS F 279 PHE 0.024 0.002 PHE A 102 TYR 0.017 0.002 TYR B 972 ARG 0.005 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 434 time to evaluate : 4.977 Fit side-chains REVERT: A 83 VAL cc_start: 0.8157 (OUTLIER) cc_final: 0.7897 (t) REVERT: A 321 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5892 (pm20) REVERT: A 350 ASP cc_start: 0.7665 (t0) cc_final: 0.7418 (t0) REVERT: A 421 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6771 (mm-30) REVERT: A 467 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7654 (pt0) REVERT: A 559 ARG cc_start: 0.7122 (mmt90) cc_final: 0.5720 (mtt180) REVERT: A 606 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8122 (tp30) REVERT: A 673 ASN cc_start: 0.8151 (m-40) cc_final: 0.7523 (t160) REVERT: A 721 ASP cc_start: 0.8498 (m-30) cc_final: 0.8261 (m-30) REVERT: A 737 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7965 (mtt-85) REVERT: A 786 ASP cc_start: 0.8894 (p0) cc_final: 0.8680 (p0) REVERT: A 1150 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 1170 ASP cc_start: 0.7641 (m-30) cc_final: 0.7269 (m-30) REVERT: A 1276 ASP cc_start: 0.7111 (t70) cc_final: 0.6560 (t0) REVERT: A 1330 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6717 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: B 46 GLU cc_start: 0.8676 (tt0) cc_final: 0.8406 (tt0) REVERT: B 51 ASP cc_start: 0.8284 (t70) cc_final: 0.7921 (m-30) REVERT: B 83 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7727 (m) REVERT: B 264 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 409 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7584 (mt0) REVERT: B 467 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 472 GLN cc_start: 0.7752 (mm110) cc_final: 0.7540 (mm110) REVERT: B 543 THR cc_start: 0.8810 (m) cc_final: 0.8379 (p) REVERT: B 567 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8162 (t) REVERT: B 675 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: B 891 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7711 (tmm-80) REVERT: B 987 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7396 (mp0) REVERT: B 1302 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 1318 GLU cc_start: 0.7344 (tt0) cc_final: 0.6617 (tp30) REVERT: B 1327 LYS cc_start: 0.7878 (mttt) cc_final: 0.7245 (pttt) REVERT: B 1352 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5677 (tt0) REVERT: B 1354 GLU cc_start: 0.7340 (tt0) cc_final: 0.6738 (mm-30) REVERT: C 46 GLU cc_start: 0.8313 (tt0) cc_final: 0.7982 (tp30) REVERT: C 51 ASP cc_start: 0.8611 (t70) cc_final: 0.8310 (m-30) REVERT: C 116 THR cc_start: 0.8127 (m) cc_final: 0.7547 (p) REVERT: C 232 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: C 606 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7439 (tt0) REVERT: C 841 ASP cc_start: 0.8696 (m-30) cc_final: 0.8494 (m-30) REVERT: C 885 SER cc_start: 0.8691 (t) cc_final: 0.8365 (p) REVERT: C 978 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: C 1090 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6541 (ttp) REVERT: C 1091 ASP cc_start: 0.6824 (m-30) cc_final: 0.6505 (p0) REVERT: C 1101 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6801 (pp) REVERT: C 1138 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6375 (pp20) REVERT: C 1150 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: C 1323 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6912 (mm) REVERT: C 1359 THR cc_start: 0.7951 (t) cc_final: 0.7525 (m) REVERT: D 83 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7901 (t) REVERT: D 321 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5897 (pm20) REVERT: D 350 ASP cc_start: 0.7669 (t0) cc_final: 0.7421 (t0) REVERT: D 467 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7655 (pt0) REVERT: D 559 ARG cc_start: 0.7124 (mmt90) cc_final: 0.5722 (mtt180) REVERT: D 567 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8064 (p) REVERT: D 606 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8049 (tp30) REVERT: D 673 ASN cc_start: 0.8153 (m-40) cc_final: 0.7525 (t160) REVERT: D 679 ASP cc_start: 0.8677 (t0) cc_final: 0.8435 (t70) REVERT: D 721 ASP cc_start: 0.8499 (m-30) cc_final: 0.8263 (m-30) REVERT: D 737 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7950 (mtt-85) REVERT: D 786 ASP cc_start: 0.8896 (p0) cc_final: 0.8681 (p0) REVERT: D 1090 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7624 (tmm) REVERT: D 1150 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: D 1170 ASP cc_start: 0.7642 (m-30) cc_final: 0.7274 (m-30) REVERT: D 1276 ASP cc_start: 0.7101 (t70) cc_final: 0.6551 (t0) REVERT: D 1330 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6614 (mmt-90) REVERT: D 1354 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: E 46 GLU cc_start: 0.8682 (tt0) cc_final: 0.8413 (tt0) REVERT: E 51 ASP cc_start: 0.8289 (t70) cc_final: 0.7924 (m-30) REVERT: E 83 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (m) REVERT: E 264 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: E 409 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7586 (mt0) REVERT: E 467 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7935 (mt-10) REVERT: E 472 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7452 (mm110) REVERT: E 473 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8582 (tt0) REVERT: E 543 THR cc_start: 0.8811 (m) cc_final: 0.8379 (p) REVERT: E 567 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (t) REVERT: E 583 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: E 675 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: E 891 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7708 (tmm-80) REVERT: E 898 ASP cc_start: 0.7394 (t0) cc_final: 0.6933 (t70) REVERT: E 987 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7359 (mp0) REVERT: E 1302 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: E 1318 GLU cc_start: 0.7341 (tt0) cc_final: 0.6614 (tp30) REVERT: E 1327 LYS cc_start: 0.7961 (mttt) cc_final: 0.7343 (pttt) REVERT: E 1329 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: E 1352 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: E 1354 GLU cc_start: 0.7332 (tt0) cc_final: 0.6706 (mm-30) REVERT: F 46 GLU cc_start: 0.8385 (tt0) cc_final: 0.7964 (tp30) REVERT: F 51 ASP cc_start: 0.8616 (t70) cc_final: 0.8312 (m-30) REVERT: F 116 THR cc_start: 0.8124 (m) cc_final: 0.7545 (p) REVERT: F 606 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7438 (tt0) REVERT: F 841 ASP cc_start: 0.8699 (m-30) cc_final: 0.8498 (m-30) REVERT: F 885 SER cc_start: 0.8691 (t) cc_final: 0.8365 (p) REVERT: F 978 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: F 1090 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6480 (ttp) REVERT: F 1091 ASP cc_start: 0.6870 (m-30) cc_final: 0.6509 (p0) REVERT: F 1101 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6824 (pp) REVERT: F 1138 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6338 (pp20) REVERT: F 1150 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: F 1323 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6734 (mm) REVERT: F 1359 THR cc_start: 0.7953 (t) cc_final: 0.7524 (m) outliers start: 211 outliers final: 137 residues processed: 605 average time/residue: 1.1072 time to fit residues: 908.4879 Evaluate side-chains 610 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 429 time to evaluate : 4.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 592 ASP Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1336 LEU Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1056 SER Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1323 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 737 ARG Chi-restraints excluded: chain D residue 822 GLU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1055 THR Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 583 GLN Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 922 THR Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1329 GLU Chi-restraints excluded: chain E residue 1336 LEU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 525 THR Chi-restraints excluded: chain F residue 567 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 675 GLN Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 764 VAL Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 THR Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 911 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1056 SER Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 0.0170 chunk 731 optimal weight: 0.4980 chunk 667 optimal weight: 4.9990 chunk 711 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 558 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 642 optimal weight: 6.9990 chunk 672 optimal weight: 20.0000 chunk 708 optimal weight: 4.9990 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 60000 Z= 0.170 Angle : 0.503 7.065 82068 Z= 0.277 Chirality : 0.045 0.149 9798 Planarity : 0.003 0.052 11058 Dihedral : 4.752 60.624 8308 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.12 % Allowed : 14.17 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 7950 helix: -1.76 (0.19), residues: 594 sheet: 0.95 (0.11), residues: 2168 loop : -0.73 (0.08), residues: 5188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1275 HIS 0.002 0.001 HIS C 279 PHE 0.019 0.001 PHE A 102 TYR 0.016 0.001 TYR C1348 ARG 0.003 0.000 ARG C1134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 469 time to evaluate : 5.026 Fit side-chains REVERT: A 83 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7803 (t) REVERT: A 320 ASP cc_start: 0.7751 (m-30) cc_final: 0.7505 (m-30) REVERT: A 321 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: A 350 ASP cc_start: 0.7608 (t0) cc_final: 0.7393 (t0) REVERT: A 421 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6768 (mm-30) REVERT: A 467 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7606 (pt0) REVERT: A 559 ARG cc_start: 0.7104 (mmt90) cc_final: 0.5698 (mtt180) REVERT: A 606 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7991 (tp30) REVERT: A 610 GLU cc_start: 0.6765 (pt0) cc_final: 0.6470 (mt-10) REVERT: A 673 ASN cc_start: 0.8102 (m-40) cc_final: 0.7465 (t160) REVERT: A 679 ASP cc_start: 0.8706 (t0) cc_final: 0.8474 (t70) REVERT: A 721 ASP cc_start: 0.8364 (m-30) cc_final: 0.8164 (m-30) REVERT: A 786 ASP cc_start: 0.8788 (p0) cc_final: 0.8504 (p0) REVERT: A 1150 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: A 1170 ASP cc_start: 0.7512 (m-30) cc_final: 0.7145 (m-30) REVERT: A 1276 ASP cc_start: 0.7075 (t70) cc_final: 0.6569 (t0) REVERT: A 1330 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6618 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: B 46 GLU cc_start: 0.8633 (tt0) cc_final: 0.8369 (tt0) REVERT: B 51 ASP cc_start: 0.8169 (t70) cc_final: 0.7843 (m-30) REVERT: B 83 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7556 (m) REVERT: B 264 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 409 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7591 (mt0) REVERT: B 467 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 472 GLN cc_start: 0.7750 (mm110) cc_final: 0.7490 (mm110) REVERT: B 543 THR cc_start: 0.8791 (m) cc_final: 0.8366 (p) REVERT: B 567 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 867 ASP cc_start: 0.8081 (t0) cc_final: 0.7644 (t70) REVERT: B 891 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7720 (tmm-80) REVERT: B 987 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7366 (mt-10) REVERT: B 1249 MET cc_start: 0.8273 (ptm) cc_final: 0.7811 (tmm) REVERT: B 1302 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: B 1318 GLU cc_start: 0.7327 (tt0) cc_final: 0.6615 (tp30) REVERT: B 1327 LYS cc_start: 0.7886 (mttt) cc_final: 0.7252 (pttt) REVERT: B 1352 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5615 (tt0) REVERT: B 1354 GLU cc_start: 0.7493 (tt0) cc_final: 0.6756 (mm-30) REVERT: C 51 ASP cc_start: 0.8628 (t70) cc_final: 0.8306 (m-30) REVERT: C 116 THR cc_start: 0.7864 (m) cc_final: 0.7328 (p) REVERT: C 232 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: C 606 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7330 (tt0) REVERT: C 841 ASP cc_start: 0.8708 (m-30) cc_final: 0.8505 (m-30) REVERT: C 885 SER cc_start: 0.8707 (t) cc_final: 0.8379 (p) REVERT: C 978 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: C 1090 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6526 (ttp) REVERT: C 1091 ASP cc_start: 0.6851 (m-30) cc_final: 0.6486 (p0) REVERT: C 1101 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6780 (pp) REVERT: C 1138 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6391 (pp20) REVERT: C 1150 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: C 1323 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6949 (mm) REVERT: C 1359 THR cc_start: 0.7946 (t) cc_final: 0.7510 (m) REVERT: D 83 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7757 (t) REVERT: D 321 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: D 350 ASP cc_start: 0.7609 (t0) cc_final: 0.7395 (t0) REVERT: D 467 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7605 (pt0) REVERT: D 559 ARG cc_start: 0.7104 (mmt90) cc_final: 0.5698 (mtt180) REVERT: D 567 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 606 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8019 (tp30) REVERT: D 673 ASN cc_start: 0.8103 (m-40) cc_final: 0.7466 (t160) REVERT: D 679 ASP cc_start: 0.8667 (t0) cc_final: 0.8434 (t70) REVERT: D 721 ASP cc_start: 0.8345 (m-30) cc_final: 0.8130 (m-30) REVERT: D 786 ASP cc_start: 0.8792 (p0) cc_final: 0.8507 (p0) REVERT: D 1090 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7651 (tmm) REVERT: D 1150 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: D 1170 ASP cc_start: 0.7514 (m-30) cc_final: 0.7148 (m-30) REVERT: D 1276 ASP cc_start: 0.7066 (t70) cc_final: 0.6565 (t0) REVERT: D 1354 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: E 46 GLU cc_start: 0.8639 (tt0) cc_final: 0.8377 (tt0) REVERT: E 51 ASP cc_start: 0.8176 (t70) cc_final: 0.7847 (m-30) REVERT: E 83 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7556 (m) REVERT: E 264 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: E 409 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7593 (mt0) REVERT: E 467 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 472 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7366 (mm110) REVERT: E 473 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: E 543 THR cc_start: 0.8792 (m) cc_final: 0.8366 (p) REVERT: E 867 ASP cc_start: 0.8083 (t0) cc_final: 0.7644 (t70) REVERT: E 891 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7702 (tmm-80) REVERT: E 898 ASP cc_start: 0.7401 (t0) cc_final: 0.6927 (t70) REVERT: E 987 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7363 (mt-10) REVERT: E 1302 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: E 1318 GLU cc_start: 0.7324 (tt0) cc_final: 0.6615 (tp30) REVERT: E 1327 LYS cc_start: 0.7925 (mttt) cc_final: 0.7293 (pttt) REVERT: E 1352 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.5726 (tt0) REVERT: E 1354 GLU cc_start: 0.7463 (tt0) cc_final: 0.6731 (mm-30) REVERT: F 46 GLU cc_start: 0.8393 (tt0) cc_final: 0.7978 (tp30) REVERT: F 51 ASP cc_start: 0.8634 (t70) cc_final: 0.8310 (m-30) REVERT: F 116 THR cc_start: 0.7857 (m) cc_final: 0.7322 (p) REVERT: F 606 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7328 (tt0) REVERT: F 841 ASP cc_start: 0.8709 (m-30) cc_final: 0.8505 (m-30) REVERT: F 885 SER cc_start: 0.8709 (t) cc_final: 0.8378 (p) REVERT: F 978 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: F 1090 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6506 (ttp) REVERT: F 1091 ASP cc_start: 0.6796 (m-30) cc_final: 0.6476 (p0) REVERT: F 1101 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6781 (pp) REVERT: F 1138 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6378 (pp20) REVERT: F 1150 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: F 1323 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6774 (mm) REVERT: F 1359 THR cc_start: 0.7947 (t) cc_final: 0.7507 (m) outliers start: 140 outliers final: 89 residues processed: 580 average time/residue: 1.0693 time to fit residues: 847.3736 Evaluate side-chains 554 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 429 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1056 SER Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1209 GLU Chi-restraints excluded: chain C residue 1323 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 583 GLN Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1056 SER Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1209 GLU Chi-restraints excluded: chain F residue 1323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 6.9990 chunk 752 optimal weight: 0.3980 chunk 459 optimal weight: 20.0000 chunk 356 optimal weight: 0.3980 chunk 522 optimal weight: 8.9990 chunk 789 optimal weight: 3.9990 chunk 726 optimal weight: 10.0000 chunk 628 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 485 optimal weight: 9.9990 chunk 385 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 GLN B 663 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 ASN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1050 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 60000 Z= 0.215 Angle : 0.538 11.918 82068 Z= 0.295 Chirality : 0.046 0.155 9798 Planarity : 0.004 0.053 11058 Dihedral : 4.871 61.173 8308 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.08 % Allowed : 14.33 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 7950 helix: -1.76 (0.19), residues: 594 sheet: 0.92 (0.11), residues: 2212 loop : -0.72 (0.08), residues: 5144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1275 HIS 0.004 0.001 HIS D1072 PHE 0.021 0.001 PHE A 102 TYR 0.016 0.002 TYR B1361 ARG 0.003 0.000 ARG F1134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15900 Ramachandran restraints generated. 7950 Oldfield, 0 Emsley, 7950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 434 time to evaluate : 5.060 Fit side-chains REVERT: A 83 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7839 (t) REVERT: A 321 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5965 (pm20) REVERT: A 350 ASP cc_start: 0.7594 (t0) cc_final: 0.7327 (t0) REVERT: A 421 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: A 467 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7615 (pt0) REVERT: A 559 ARG cc_start: 0.7104 (mmt90) cc_final: 0.5708 (mtt180) REVERT: A 606 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8099 (tp30) REVERT: A 673 ASN cc_start: 0.8101 (m-40) cc_final: 0.7462 (t160) REVERT: A 679 ASP cc_start: 0.8696 (t0) cc_final: 0.8462 (t70) REVERT: A 721 ASP cc_start: 0.8479 (m-30) cc_final: 0.8274 (m-30) REVERT: A 786 ASP cc_start: 0.8796 (p0) cc_final: 0.8569 (p0) REVERT: A 1150 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: A 1170 ASP cc_start: 0.7574 (m-30) cc_final: 0.7196 (m-30) REVERT: A 1276 ASP cc_start: 0.7065 (t70) cc_final: 0.6557 (t0) REVERT: A 1330 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6555 (mmt-90) REVERT: A 1354 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: B 46 GLU cc_start: 0.8652 (tt0) cc_final: 0.8388 (tt0) REVERT: B 51 ASP cc_start: 0.8313 (t70) cc_final: 0.7954 (m-30) REVERT: B 83 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7603 (m) REVERT: B 409 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7615 (mt0) REVERT: B 467 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 472 GLN cc_start: 0.7740 (mm110) cc_final: 0.7476 (mm110) REVERT: B 543 THR cc_start: 0.8791 (m) cc_final: 0.8363 (p) REVERT: B 567 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 583 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: B 867 ASP cc_start: 0.8052 (t0) cc_final: 0.7640 (t70) REVERT: B 891 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7721 (tmm-80) REVERT: B 987 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7324 (mp0) REVERT: B 1219 ASP cc_start: 0.6050 (m-30) cc_final: 0.5810 (m-30) REVERT: B 1249 MET cc_start: 0.8283 (ptm) cc_final: 0.7814 (tmm) REVERT: B 1302 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: B 1318 GLU cc_start: 0.7365 (tt0) cc_final: 0.6608 (tp30) REVERT: B 1327 LYS cc_start: 0.7849 (mttt) cc_final: 0.7235 (pttt) REVERT: B 1352 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5684 (tt0) REVERT: B 1354 GLU cc_start: 0.7480 (tt0) cc_final: 0.6785 (mm-30) REVERT: C 51 ASP cc_start: 0.8629 (t70) cc_final: 0.8324 (m-30) REVERT: C 116 THR cc_start: 0.7935 (m) cc_final: 0.7410 (p) REVERT: C 232 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: C 606 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7327 (tt0) REVERT: C 841 ASP cc_start: 0.8691 (m-30) cc_final: 0.8489 (m-30) REVERT: C 885 SER cc_start: 0.8754 (t) cc_final: 0.8428 (p) REVERT: C 978 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: C 1090 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6605 (ttp) REVERT: C 1091 ASP cc_start: 0.6844 (m-30) cc_final: 0.6534 (p0) REVERT: C 1101 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6759 (pp) REVERT: C 1138 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6358 (pp20) REVERT: C 1150 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: C 1359 THR cc_start: 0.7946 (t) cc_final: 0.7512 (m) REVERT: D 83 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7846 (t) REVERT: D 321 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5980 (pm20) REVERT: D 350 ASP cc_start: 0.7595 (t0) cc_final: 0.7329 (t0) REVERT: D 467 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7615 (pt0) REVERT: D 559 ARG cc_start: 0.7106 (mmt90) cc_final: 0.5709 (mtt180) REVERT: D 567 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.7970 (p) REVERT: D 606 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8019 (tp30) REVERT: D 673 ASN cc_start: 0.8103 (m-40) cc_final: 0.7463 (t160) REVERT: D 679 ASP cc_start: 0.8655 (t0) cc_final: 0.8422 (t70) REVERT: D 721 ASP cc_start: 0.8484 (m-30) cc_final: 0.8261 (m-30) REVERT: D 786 ASP cc_start: 0.8799 (p0) cc_final: 0.8571 (p0) REVERT: D 1090 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: D 1150 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: D 1170 ASP cc_start: 0.7573 (m-30) cc_final: 0.7197 (m-30) REVERT: D 1276 ASP cc_start: 0.7052 (t70) cc_final: 0.6548 (t0) REVERT: D 1354 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: E 46 GLU cc_start: 0.8658 (tt0) cc_final: 0.8393 (tt0) REVERT: E 51 ASP cc_start: 0.8315 (t70) cc_final: 0.7955 (m-30) REVERT: E 83 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7604 (m) REVERT: E 409 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7650 (mt0) REVERT: E 467 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7905 (mt-10) REVERT: E 472 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7456 (mm110) REVERT: E 473 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: E 543 THR cc_start: 0.8792 (m) cc_final: 0.8363 (p) REVERT: E 567 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8117 (t) REVERT: E 867 ASP cc_start: 0.8055 (t0) cc_final: 0.7643 (t70) REVERT: E 891 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7721 (tmm-80) REVERT: E 898 ASP cc_start: 0.7382 (t0) cc_final: 0.6916 (t70) REVERT: E 987 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7325 (mp0) REVERT: E 1219 ASP cc_start: 0.6122 (m-30) cc_final: 0.5886 (m-30) REVERT: E 1302 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: E 1318 GLU cc_start: 0.7336 (tt0) cc_final: 0.6595 (tp30) REVERT: E 1327 LYS cc_start: 0.7936 (mttt) cc_final: 0.7299 (pttt) REVERT: E 1352 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5633 (tt0) REVERT: E 1354 GLU cc_start: 0.7382 (tt0) cc_final: 0.6678 (mm-30) REVERT: F 46 GLU cc_start: 0.8396 (tt0) cc_final: 0.7979 (tp30) REVERT: F 51 ASP cc_start: 0.8634 (t70) cc_final: 0.8321 (m-30) REVERT: F 116 THR cc_start: 0.7930 (m) cc_final: 0.7406 (p) REVERT: F 606 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7327 (tt0) REVERT: F 841 ASP cc_start: 0.8695 (m-30) cc_final: 0.8493 (m-30) REVERT: F 885 SER cc_start: 0.8756 (t) cc_final: 0.8428 (p) REVERT: F 978 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: F 1090 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6465 (ttp) REVERT: F 1091 ASP cc_start: 0.6786 (m-30) cc_final: 0.6540 (p0) REVERT: F 1101 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6785 (pp) REVERT: F 1138 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6362 (pp20) REVERT: F 1150 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: F 1323 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6747 (mm) REVERT: F 1359 THR cc_start: 0.7947 (t) cc_final: 0.7511 (m) outliers start: 137 outliers final: 95 residues processed: 543 average time/residue: 1.0967 time to fit residues: 808.0529 Evaluate side-chains 554 residues out of total 6600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 424 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1356 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 583 GLN Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 737 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 891 ARG Chi-restraints excluded: chain B residue 959 SER Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1017 SER Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1302 ASP Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1056 SER Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1107 VAL Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1153 VAL Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1209 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 583 GLN Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1090 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1356 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 472 GLN Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 567 THR Chi-restraints excluded: chain E residue 592 ASP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 654 ASN Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 724 SER Chi-restraints excluded: chain E residue 737 ARG Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 839 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 891 ARG Chi-restraints excluded: chain E residue 959 SER Chi-restraints excluded: chain E residue 1017 SER Chi-restraints excluded: chain E residue 1070 THR Chi-restraints excluded: chain E residue 1101 ILE Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1228 THR Chi-restraints excluded: chain E residue 1302 ASP Chi-restraints excluded: chain E residue 1324 SER Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 571 SER Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 813 VAL Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 978 GLU Chi-restraints excluded: chain F residue 1056 SER Chi-restraints excluded: chain F residue 1090 MET Chi-restraints excluded: chain F residue 1101 ILE Chi-restraints excluded: chain F residue 1107 VAL Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1153 VAL Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1209 GLU Chi-restraints excluded: chain F residue 1323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 10.0000 chunk 669 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 579 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 629 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 646 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 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 = 0.3620 r_free = 0.3620 target = 0.127880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108957 restraints weight = 85066.045| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.42 r_work: 0.3292 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 60000 Z= 0.277 Angle : 0.582 11.935 82068 Z= 0.319 Chirality : 0.047 0.164 9798 Planarity : 0.004 0.053 11058 Dihedral : 5.102 61.557 8308 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.47 % Allowed : 14.11 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 7950 helix: -1.88 (0.19), residues: 594 sheet: 0.84 (0.11), residues: 2204 loop : -0.77 (0.08), residues: 5152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1275 HIS 0.004 0.001 HIS C 279 PHE 0.022 0.002 PHE A 102 TYR 0.016 0.002 TYR A 763 ARG 0.004 0.001 ARG C1117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15511.14 seconds wall clock time: 270 minutes 30.79 seconds (16230.79 seconds total)