Starting phenix.real_space_refine on Sat Sep 28 21:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c8m_16484/09_2024/8c8m_16484.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.422 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 114 5.16 5 C 43404 2.51 5 N 11328 2.21 5 O 15660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 659 residue(s): 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70506 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Chain: "B" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Chain: "C" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Chain: "D" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Chain: "E" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Chain: "F" Number of atoms: 11751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 11751 Classifications: {'peptide': 1580} Link IDs: {'PCIS': 5, 'PTRANS': 46, 'TRANS': 1528} Time building chain proxies: 31.72, per 1000 atoms: 0.45 Number of scatterers: 70506 At special positions: 0 Unit cell: (243.516, 258.804, 126.672, 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 114 16.00 O 15660 8.00 N 11328 7.00 C 43404 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: 13.10 Conformation dependent library (CDL) restraints added in 7.2 seconds 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17280 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 168 sheets defined 11.3% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.05 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 'A' and resid 1389 through 1392 Processing helix chain 'A' and resid 1523 through 1526 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 'B' and resid 1389 through 1392 Processing helix chain 'B' and resid 1523 through 1526 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 'C' and resid 1389 through 1392 Processing helix chain 'C' and resid 1523 through 1526 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 'D' and resid 1389 through 1392 Processing helix chain 'D' and resid 1523 through 1526 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 'E' and resid 1389 through 1392 Processing helix chain 'E' and resid 1523 through 1526 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 helix chain 'F' and resid 1389 through 1392 Processing helix chain 'F' and resid 1523 through 1526 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 'A' and resid 1368 through 1371 Processing sheet with id=AC7, first strand: chain 'A' and resid 1368 through 1371 removed outlier: 3.869A pdb=" N GLY A1468 " --> pdb=" O GLU A1436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1375 through 1376 removed outlier: 7.576A pdb=" N GLU A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A1484 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL A1518 " --> pdb=" O GLY A1564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1564 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR A1565 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A1551 " --> pdb=" O THR A1565 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE A1567 " --> pdb=" O ASP A1549 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ASP A1549 " --> pdb=" O PHE A1567 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLU A1536 " --> pdb=" O GLU A1592 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1592 " --> pdb=" O GLU A1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1585 " --> pdb=" O ILE A1614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1614 " --> pdb=" O ASP A1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1606 " --> pdb=" O ASP A1593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL A1518 " --> pdb=" O GLY A1564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A1564 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU A1579 " --> pdb=" O THR A1565 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A1567 " --> pdb=" O LEU A1579 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AD3, 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=AD4, 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=AD5, 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=AD6, 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=AD7, 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=AD8, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AD9, first strand: chain 'B' and resid 458 through 461 Processing sheet with id=AE1, 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=AE2, 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=AE3, 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=AE4, 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=AE5, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AE6, 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=AE7, 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=AE8, 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=AE9, first strand: chain 'B' and resid 960 through 961 Processing sheet with id=AF1, 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=AF2, 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=AF3, 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=AF4, first strand: chain 'B' and resid 1162 through 1163 Processing sheet with id=AF5, 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=AF6, first strand: chain 'B' and resid 1242 through 1243 Processing sheet with id=AF7, first strand: chain 'B' and resid 1368 through 1371 Processing sheet with id=AF8, first strand: chain 'B' and resid 1368 through 1371 removed outlier: 3.863A pdb=" N GLY B1468 " --> pdb=" O GLU B1436 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 1375 through 1376 removed outlier: 7.562A pdb=" N GLU B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B1484 " --> pdb=" O GLU B1488 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL B1518 " --> pdb=" O GLY B1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B1564 " --> pdb=" O VAL B1518 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR B1565 " --> pdb=" O THR B1551 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B1551 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N PHE B1567 " --> pdb=" O ASP B1549 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N ASP B1549 " --> pdb=" O PHE B1567 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU B1536 " --> pdb=" O GLU B1592 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B1592 " --> pdb=" O GLU B1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B1585 " --> pdb=" O ILE B1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B1614 " --> pdb=" O ASP B1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B1606 " --> pdb=" O ASP B1593 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL B1518 " --> pdb=" O GLY B1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B1564 " --> pdb=" O VAL B1518 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU B1579 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE B1567 " --> pdb=" O LEU B1579 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AG4, 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=AG5, 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=AG6, 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=AG7, 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=AG8, 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=AG9, first strand: chain 'C' and resid 372 through 373 Processing sheet with id=AH1, first strand: chain 'C' and resid 458 through 461 Processing sheet with id=AH2, 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=AH3, 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=AH4, 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=AH5, 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=AH6, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AH7, 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=AH8, 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=AH9, 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=AI1, first strand: chain 'C' and resid 960 through 961 Processing sheet with id=AI2, 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=AI3, 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=AI4, 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=AI5, first strand: chain 'C' and resid 1162 through 1163 Processing sheet with id=AI6, 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=AI7, first strand: chain 'C' and resid 1242 through 1243 Processing sheet with id=AI8, first strand: chain 'C' and resid 1368 through 1371 Processing sheet with id=AI9, first strand: chain 'C' and resid 1368 through 1371 removed outlier: 3.865A pdb=" N GLY C1468 " --> pdb=" O GLU C1436 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 1375 through 1376 removed outlier: 7.555A pdb=" N GLU C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C1484 " --> pdb=" O GLU C1488 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL C1518 " --> pdb=" O GLY C1564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C1564 " --> pdb=" O VAL C1518 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR C1565 " --> pdb=" O THR C1551 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C1551 " --> pdb=" O THR C1565 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N PHE C1567 " --> pdb=" O ASP C1549 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N ASP C1549 " --> pdb=" O PHE C1567 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU C1536 " --> pdb=" O GLU C1592 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C1592 " --> pdb=" O GLU C1536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C1585 " --> pdb=" O ILE C1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C1614 " --> pdb=" O ASP C1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C1606 " --> pdb=" O ASP C1593 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 1502 through 1505 removed outlier: 3.514A pdb=" N VAL C1518 " --> pdb=" O GLY C1564 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C1564 " --> pdb=" O VAL C1518 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU C1579 " --> pdb=" O THR C1565 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1567 " --> pdb=" O LEU C1579 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 41 through 43 Processing sheet with id=AJ5, 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=AJ6, 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=AJ7, 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=AJ8, 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=AJ9, 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=AK1, first strand: chain 'D' and resid 372 through 373 Processing sheet with id=AK2, first strand: chain 'D' and resid 458 through 461 Processing sheet with id=AK3, 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=AK4, 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=AK5, 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=AK6, 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=AK7, first strand: chain 'D' and resid 527 through 529 Processing sheet with id=AK8, 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=AK9, 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=AL1, 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=AL2, first strand: chain 'D' and resid 960 through 961 Processing sheet with id=AL3, 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=AL4, 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=AL5, 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=AL6, first strand: chain 'D' and resid 1162 through 1163 Processing sheet with id=AL7, 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=AL8, first strand: chain 'D' and resid 1242 through 1243 Processing sheet with id=AL9, first strand: chain 'D' and resid 1368 through 1371 Processing sheet with id=AM1, first strand: chain 'D' and resid 1368 through 1371 removed outlier: 3.868A pdb=" N GLY D1468 " --> pdb=" O GLU D1436 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'D' and resid 1375 through 1376 removed outlier: 7.561A pdb=" N GLU D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D1484 " --> pdb=" O GLU D1488 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'D' and resid 1502 through 1505 removed outlier: 3.515A pdb=" N VAL D1518 " --> pdb=" O GLY D1564 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D1564 " --> pdb=" O VAL D1518 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR D1565 " --> pdb=" O THR D1551 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR D1551 " --> pdb=" O THR D1565 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE D1567 " --> pdb=" O ASP D1549 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ASP D1549 " --> pdb=" O PHE D1567 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU D1536 " --> pdb=" O GLU D1592 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU D1592 " --> pdb=" O GLU D1536 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP D1585 " --> pdb=" O ILE D1614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D1614 " --> pdb=" O ASP D1585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D1606 " --> pdb=" O ASP D1593 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'D' and resid 1502 through 1505 removed outlier: 3.515A pdb=" N VAL D1518 " --> pdb=" O GLY D1564 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D1564 " --> pdb=" O VAL D1518 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU D1579 " --> pdb=" O THR D1565 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D1567 " --> pdb=" O LEU D1579 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AM6, 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=AM7, 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=AM8, 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=AM9, 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=AN1, 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=AN2, first strand: chain 'E' and resid 372 through 373 Processing sheet with id=AN3, first strand: chain 'E' and resid 458 through 461 Processing sheet with id=AN4, 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=AN5, 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=AN6, 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=AN7, 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=AN8, first strand: chain 'E' and resid 527 through 529 Processing sheet with id=AN9, 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=AO1, 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=AO2, 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=AO3, first strand: chain 'E' and resid 960 through 961 Processing sheet with id=AO4, 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=AO5, 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=AO6, 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=AO7, first strand: chain 'E' and resid 1162 through 1163 Processing sheet with id=AO8, 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=AO9, first strand: chain 'E' and resid 1242 through 1243 Processing sheet with id=AP1, first strand: chain 'E' and resid 1368 through 1371 Processing sheet with id=AP2, first strand: chain 'E' and resid 1368 through 1371 removed outlier: 3.864A pdb=" N GLY E1468 " --> pdb=" O GLU E1436 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'E' and resid 1375 through 1376 removed outlier: 7.562A pdb=" N GLU E1488 " --> pdb=" O PHE E1484 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE E1484 " --> pdb=" O GLU E1488 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 3.516A pdb=" N VAL E1518 " --> pdb=" O GLY E1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E1564 " --> pdb=" O VAL E1518 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR E1565 " --> pdb=" O THR E1551 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E1551 " --> pdb=" O THR E1565 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N PHE E1567 " --> pdb=" O ASP E1549 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N ASP E1549 " --> pdb=" O PHE E1567 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU E1536 " --> pdb=" O GLU E1592 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU E1592 " --> pdb=" O GLU E1536 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP E1585 " --> pdb=" O ILE E1614 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1614 " --> pdb=" O ASP E1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E1606 " --> pdb=" O ASP E1593 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 3.516A pdb=" N VAL E1518 " --> pdb=" O GLY E1564 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E1564 " --> pdb=" O VAL E1518 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU E1579 " --> pdb=" O THR E1565 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE E1567 " --> pdb=" O LEU E1579 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'F' and resid 41 through 43 Processing sheet with id=AP7, 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=AP8, 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=AP9, 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=AQ1, 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=AQ2, 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=AQ3, first strand: chain 'F' and resid 372 through 373 Processing sheet with id=AQ4, first strand: chain 'F' and resid 458 through 461 Processing sheet with id=AQ5, 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=AQ6, 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=AQ7, 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=AQ8, 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=AQ9, first strand: chain 'F' and resid 527 through 529 Processing sheet with id=AR1, 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=AR2, 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=AR3, 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=AR4, first strand: chain 'F' and resid 960 through 961 Processing sheet with id=AR5, 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=AR6, 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=AR7, 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=AR8, first strand: chain 'F' and resid 1162 through 1163 Processing sheet with id=AR9, 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=AS1, first strand: chain 'F' and resid 1242 through 1243 Processing sheet with id=AS2, first strand: chain 'F' and resid 1368 through 1371 Processing sheet with id=AS3, first strand: chain 'F' and resid 1368 through 1371 removed outlier: 3.865A pdb=" N GLY F1468 " --> pdb=" O GLU F1436 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'F' and resid 1375 through 1376 removed outlier: 7.555A pdb=" N GLU F1488 " --> pdb=" O PHE F1484 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F1484 " --> pdb=" O GLU F1488 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'F' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL F1518 " --> pdb=" O GLY F1564 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F1564 " --> pdb=" O VAL F1518 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR F1565 " --> pdb=" O THR F1551 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR F1551 " --> pdb=" O THR F1565 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N PHE F1567 " --> pdb=" O ASP F1549 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N ASP F1549 " --> pdb=" O PHE F1567 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU F1536 " --> pdb=" O GLU F1592 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU F1592 " --> pdb=" O GLU F1536 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP F1585 " --> pdb=" O ILE F1614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F1614 " --> pdb=" O ASP F1585 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F1606 " --> pdb=" O ASP F1593 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'F' and resid 1502 through 1505 removed outlier: 3.513A pdb=" N VAL F1518 " --> pdb=" O GLY F1564 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY F1564 " --> pdb=" O VAL F1518 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LEU F1579 " --> pdb=" O THR F1565 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE F1567 " --> pdb=" O LEU F1579 " (cutoff:3.500A) 2412 hydrogen bonds defined for protein. 5922 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: 62.96 Time building geometry restraints manager: 15.84 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: 1872 1.22 - 1.38: 24522 1.38 - 1.54: 44178 1.54 - 1.69: 894 1.69 - 1.85: 180 Bond restraints: 71646 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 71641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 95701 3.63 - 7.27: 2246 7.27 - 10.90: 67 10.90 - 14.54: 18 14.54 - 18.17: 2 Bond angle restraints: 98034 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 98029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 38417 17.77 - 35.53: 3138 35.53 - 53.30: 420 53.30 - 71.06: 122 71.06 - 88.83: 53 Dihedral angle restraints: 42150 sinusoidal: 15192 harmonic: 26958 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 42147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 7247 0.076 - 0.153: 3812 0.153 - 0.229: 536 0.229 - 0.306: 72 0.306 - 0.382: 15 Chirality restraints: 11682 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 11679 not shown) Planarity restraints: 13194 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 13191 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 27 1.90 - 2.65: 1475 2.65 - 3.40: 93265 3.40 - 4.15: 177189 4.15 - 4.90: 316445 Nonbonded interactions: 588401 Sorted by model distance: nonbonded pdb=" OE1 GLU A 196 " pdb=" OE1 GLU F 143 " model vdw 1.144 3.040 nonbonded pdb=" OE2 GLU D1352 " pdb=" CZ ARG E1578 " model vdw 1.232 3.270 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 ... (remaining 588396 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: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.090 Check model and map are aligned: 0.440 Set scattering table: 0.500 Process input model: 171.830 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.350 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 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 71646 Z= 0.928 Angle : 1.574 18.173 98034 Z= 1.100 Chirality : 0.083 0.382 11682 Planarity : 0.008 0.092 13194 Dihedral : 13.685 88.830 24798 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.74 % Allowed : 4.27 % Favored : 94.99 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 9.80 % 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: -1.25 (0.08), residues: 9468 helix: -2.68 (0.16), residues: 624 sheet: 0.31 (0.10), residues: 2746 loop : -1.21 (0.07), residues: 6098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.009 TRP E 286 HIS 0.029 0.006 HIS B1577 PHE 0.074 0.008 PHE D1393 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) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 950 time to evaluate : 5.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASP cc_start: 0.9050 (t0) cc_final: 0.8773 (t0) REVERT: A 635 ASP cc_start: 0.9355 (m-30) cc_final: 0.9122 (m-30) REVERT: A 1032 ASP cc_start: 0.8528 (m-30) cc_final: 0.8302 (p0) REVERT: A 1170 ASP cc_start: 0.8601 (m-30) cc_final: 0.8243 (m-30) REVERT: A 1330 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (mmt-90) REVERT: A 1406 SER cc_start: 0.9348 (m) cc_final: 0.9124 (m) REVERT: A 1452 ASN cc_start: 0.8267 (p0) cc_final: 0.7983 (p0) REVERT: B 74 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 80 ASP cc_start: 0.8941 (t70) cc_final: 0.8606 (p0) REVERT: B 606 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8916 (tp30) REVERT: B 978 GLU cc_start: 0.8448 (pm20) cc_final: 0.8188 (pm20) REVERT: B 1029 THR cc_start: 0.9245 (p) cc_final: 0.8963 (p) REVERT: B 1219 ASP cc_start: 0.6757 (m-30) cc_final: 0.6510 (p0) REVERT: B 1237 GLN cc_start: 0.8780 (pt0) cc_final: 0.8521 (pt0) REVERT: B 1354 GLU cc_start: 0.8820 (tt0) cc_final: 0.8391 (tm-30) REVERT: B 1407 ASP cc_start: 0.8656 (t70) cc_final: 0.8323 (p0) REVERT: B 1414 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8083 (mpt-90) REVERT: B 1417 ASP cc_start: 0.8585 (p0) cc_final: 0.8333 (p0) REVERT: B 1486 GLU cc_start: 0.8195 (tt0) cc_final: 0.7879 (tp30) REVERT: B 1536 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7954 (mp0) REVERT: C 71 ASP cc_start: 0.8807 (p0) cc_final: 0.8527 (t0) REVERT: C 199 ASP cc_start: 0.8731 (m-30) cc_final: 0.8526 (m-30) REVERT: C 565 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7537 (p0) REVERT: C 797 ASP cc_start: 0.9182 (t0) cc_final: 0.8944 (t0) REVERT: C 1029 THR cc_start: 0.9119 (p) cc_final: 0.8697 (p) REVERT: C 1032 ASP cc_start: 0.8135 (m-30) cc_final: 0.7753 (p0) REVERT: C 1097 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8858 (ttmm) REVERT: C 1105 ASP cc_start: 0.8706 (t0) cc_final: 0.8428 (t0) REVERT: C 1230 ASP cc_start: 0.8193 (t0) cc_final: 0.7916 (t0) REVERT: C 1263 ASP cc_start: 0.7925 (t0) cc_final: 0.7603 (p0) REVERT: C 1414 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8147 (mtt90) REVERT: C 1417 ASP cc_start: 0.8850 (p0) cc_final: 0.8493 (p0) REVERT: C 1420 ASN cc_start: 0.8722 (m-40) cc_final: 0.8478 (m-40) REVERT: C 1486 GLU cc_start: 0.8271 (tt0) cc_final: 0.7981 (tp30) REVERT: C 1536 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7791 (mp0) REVERT: D 466 ASP cc_start: 0.9071 (t0) cc_final: 0.8806 (t0) REVERT: D 635 ASP cc_start: 0.9358 (m-30) cc_final: 0.9131 (m-30) REVERT: D 1057 THR cc_start: 0.7934 (p) cc_final: 0.7705 (t) REVERT: D 1170 ASP cc_start: 0.8584 (m-30) cc_final: 0.8218 (m-30) REVERT: D 1190 ASP cc_start: 0.8055 (t0) cc_final: 0.7649 (m-30) REVERT: D 1248 ASP cc_start: 0.8587 (m-30) cc_final: 0.7799 (p0) REVERT: D 1327 LYS cc_start: 0.9420 (mttt) cc_final: 0.9208 (mmtt) REVERT: D 1330 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8215 (mmt-90) REVERT: D 1486 GLU cc_start: 0.8172 (tt0) cc_final: 0.7955 (pt0) REVERT: E 74 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7983 (mt-10) REVERT: E 80 ASP cc_start: 0.8908 (t70) cc_final: 0.8600 (p0) REVERT: E 841 ASP cc_start: 0.9100 (m-30) cc_final: 0.8896 (m-30) REVERT: E 978 GLU cc_start: 0.8456 (pm20) cc_final: 0.8198 (pm20) REVERT: E 1029 THR cc_start: 0.9237 (p) cc_final: 0.8968 (p) REVERT: E 1032 ASP cc_start: 0.8759 (m-30) cc_final: 0.8556 (p0) REVERT: E 1237 GLN cc_start: 0.8811 (pt0) cc_final: 0.8559 (pt0) REVERT: E 1354 GLU cc_start: 0.8803 (tt0) cc_final: 0.8358 (tm-30) REVERT: E 1407 ASP cc_start: 0.8639 (t70) cc_final: 0.8298 (p0) REVERT: E 1414 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7979 (mpt-90) REVERT: E 1417 ASP cc_start: 0.8566 (p0) cc_final: 0.8318 (p0) REVERT: E 1536 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7924 (mp0) REVERT: F 565 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7551 (p0) REVERT: F 797 ASP cc_start: 0.9175 (t0) cc_final: 0.8939 (t0) REVERT: F 867 ASP cc_start: 0.8918 (t0) cc_final: 0.8630 (t0) REVERT: F 1029 THR cc_start: 0.9133 (p) cc_final: 0.8706 (p) REVERT: F 1032 ASP cc_start: 0.8174 (m-30) cc_final: 0.7781 (p0) REVERT: F 1097 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8892 (ttmm) REVERT: F 1105 ASP cc_start: 0.8703 (t0) cc_final: 0.8428 (t0) REVERT: F 1263 ASP cc_start: 0.7920 (t0) cc_final: 0.7588 (p0) REVERT: F 1414 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8117 (mtt90) REVERT: F 1417 ASP cc_start: 0.8845 (p0) cc_final: 0.8476 (p0) REVERT: F 1420 ASN cc_start: 0.8719 (m-40) cc_final: 0.8456 (m-40) REVERT: F 1536 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7755 (mp0) outliers start: 58 outliers final: 13 residues processed: 1005 average time/residue: 1.2651 time to fit residues: 1753.1147 Evaluate side-chains 542 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 521 time to evaluate : 6.372 ------------------------------------------------------------------------------- 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 1414 ARG Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 565 ASN Chi-restraints excluded: chain C residue 1414 ARG Chi-restraints excluded: chain D residue 269 ARG 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 1414 ARG Chi-restraints excluded: chain F residue 565 ASN Chi-restraints excluded: chain F residue 1414 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 2.9990 chunk 718 optimal weight: 0.0770 chunk 398 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 484 optimal weight: 0.8980 chunk 383 optimal weight: 6.9990 chunk 743 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 451 optimal weight: 2.9990 chunk 553 optimal weight: 3.9990 chunk 860 optimal weight: 0.8980 overall best weight: 1.1140 ------------------------------------------------------------------------------- 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 409 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 GLN A 804 ASN A 956 GLN A1154 ASN A1167 ASN A1391 HIS B 84 ASN B 92 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 409 GLN B 565 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN B 733 GLN B 804 ASN B 956 GLN B1391 HIS C 38 ASN C 58 GLN 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 C1050 HIS C1391 HIS D 38 ASN D 58 GLN D 92 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 409 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 733 GLN D 804 ASN D 956 GLN D1154 ASN D1167 ASN D1391 HIS E 84 ASN E 92 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN E 409 GLN E 565 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN E 733 GLN E 804 ASN E 956 GLN E1391 HIS F 40 ASN F 58 GLN F 92 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN F 617 ASN ** F 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 733 GLN F 804 ASN F1050 HIS F1391 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 71646 Z= 0.170 Angle : 0.555 10.975 98034 Z= 0.306 Chirality : 0.046 0.167 11682 Planarity : 0.004 0.054 13194 Dihedral : 5.425 80.487 9948 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 9.69 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.74 (0.08), residues: 9468 helix: -2.32 (0.17), residues: 690 sheet: 0.63 (0.10), residues: 2850 loop : -0.85 (0.07), residues: 5928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F1275 HIS 0.007 0.001 HIS F1050 PHE 0.014 0.001 PHE F 102 TYR 0.016 0.001 TYR F1268 ARG 0.005 0.000 ARG D1578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 637 time to evaluate : 6.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASP cc_start: 0.8585 (t0) cc_final: 0.8351 (t70) REVERT: A 466 ASP cc_start: 0.9088 (t0) cc_final: 0.8848 (t0) REVERT: A 565 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7461 (p0) REVERT: A 673 ASN cc_start: 0.8565 (m-40) cc_final: 0.8247 (t160) REVERT: A 1170 ASP cc_start: 0.8696 (m-30) cc_final: 0.8367 (m-30) REVERT: A 1330 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8192 (mmt-90) REVERT: B 264 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: B 606 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9048 (tp30) REVERT: B 835 ASP cc_start: 0.8452 (m-30) cc_final: 0.8090 (t0) REVERT: B 978 GLU cc_start: 0.8424 (pm20) cc_final: 0.7944 (pm20) REVERT: B 987 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8281 (mp0) REVERT: B 1237 GLN cc_start: 0.8637 (pt0) cc_final: 0.8380 (pt0) REVERT: B 1354 GLU cc_start: 0.8740 (tt0) cc_final: 0.8279 (tm-30) REVERT: C 66 ASP cc_start: 0.8391 (t0) cc_final: 0.8035 (t0) REVERT: C 68 ASP cc_start: 0.8894 (m-30) cc_final: 0.8676 (m-30) REVERT: C 71 ASP cc_start: 0.8833 (p0) cc_final: 0.8577 (p0) REVERT: C 797 ASP cc_start: 0.9241 (t0) cc_final: 0.8983 (t0) REVERT: C 885 SER cc_start: 0.9423 (t) cc_final: 0.9180 (p) REVERT: C 1105 ASP cc_start: 0.8509 (t0) cc_final: 0.8272 (t0) REVERT: C 1337 GLU cc_start: 0.8856 (tt0) cc_final: 0.8523 (tt0) REVERT: C 1420 ASN cc_start: 0.8596 (m-40) cc_final: 0.8315 (m-40) REVERT: D 460 ASP cc_start: 0.8577 (t0) cc_final: 0.8330 (t70) REVERT: D 466 ASP cc_start: 0.9103 (t0) cc_final: 0.8882 (t0) REVERT: D 565 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7476 (p0) REVERT: D 673 ASN cc_start: 0.8563 (m-40) cc_final: 0.8236 (t160) REVERT: D 1170 ASP cc_start: 0.8692 (m-30) cc_final: 0.8352 (m-30) REVERT: D 1190 ASP cc_start: 0.8172 (t0) cc_final: 0.7838 (m-30) REVERT: E 835 ASP cc_start: 0.8438 (m-30) cc_final: 0.8098 (t0) REVERT: E 978 GLU cc_start: 0.8425 (pm20) cc_final: 0.7945 (pm20) REVERT: E 987 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8284 (mp0) REVERT: E 1105 ASP cc_start: 0.8969 (t0) cc_final: 0.8744 (t0) REVERT: E 1237 GLN cc_start: 0.8662 (pt0) cc_final: 0.8406 (pt0) REVERT: E 1354 GLU cc_start: 0.8734 (tt0) cc_final: 0.8279 (tm-30) REVERT: F 66 ASP cc_start: 0.8446 (t0) cc_final: 0.8114 (t0) REVERT: F 797 ASP cc_start: 0.9253 (t0) cc_final: 0.8986 (t0) REVERT: F 885 SER cc_start: 0.9423 (t) cc_final: 0.9183 (p) REVERT: F 1170 ASP cc_start: 0.8401 (m-30) cc_final: 0.8067 (m-30) REVERT: F 1337 GLU cc_start: 0.8756 (tt0) cc_final: 0.8444 (tt0) REVERT: F 1420 ASN cc_start: 0.8586 (m-40) cc_final: 0.8283 (m-40) outliers start: 111 outliers final: 37 residues processed: 716 average time/residue: 1.2070 time to fit residues: 1217.1483 Evaluate side-chains 513 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 472 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 ASN Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1330 ARG Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1406 SER Chi-restraints excluded: chain B residue 1486 GLU Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1302 ASP Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1406 SER Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain D residue 565 ASN Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1194 SER Chi-restraints excluded: chain D residue 1308 ASP Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1406 SER Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 793 GLU Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1406 SER Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1302 ASP Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1406 SER Chi-restraints excluded: chain F residue 1520 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 716 optimal weight: 0.8980 chunk 586 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 862 optimal weight: 8.9990 chunk 931 optimal weight: 20.0000 chunk 768 optimal weight: 7.9990 chunk 855 optimal weight: 10.0000 chunk 294 optimal weight: 0.0570 chunk 691 optimal weight: 10.0000 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 409 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 565 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 38 ASN C 40 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN C1452 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 565 ASN ** E 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 71646 Z= 0.219 Angle : 0.537 10.602 98034 Z= 0.293 Chirality : 0.046 0.166 11682 Planarity : 0.003 0.047 13194 Dihedral : 4.808 67.241 9900 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.66 % Allowed : 11.38 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.62 (0.08), residues: 9468 helix: -2.13 (0.17), residues: 690 sheet: 0.65 (0.10), residues: 2920 loop : -0.75 (0.08), residues: 5858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F1275 HIS 0.003 0.001 HIS F 279 PHE 0.015 0.001 PHE A 124 TYR 0.017 0.001 TYR F1268 ARG 0.005 0.000 ARG D1578 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 549 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASP cc_start: 0.8867 (t0) cc_final: 0.8592 (t70) REVERT: A 466 ASP cc_start: 0.9062 (t0) cc_final: 0.8821 (t0) REVERT: A 720 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8716 (mtt) REVERT: A 1150 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: A 1170 ASP cc_start: 0.8644 (m-30) cc_final: 0.8319 (m-30) REVERT: A 1407 ASP cc_start: 0.8929 (t70) cc_final: 0.8658 (p0) REVERT: B 264 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: B 472 GLN cc_start: 0.8143 (mt0) cc_final: 0.7872 (mm110) REVERT: B 592 ASP cc_start: 0.7603 (t0) cc_final: 0.7402 (t0) REVERT: B 606 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9108 (tp30) REVERT: B 835 ASP cc_start: 0.8278 (m-30) cc_final: 0.8070 (t0) REVERT: B 978 GLU cc_start: 0.8505 (pm20) cc_final: 0.8167 (pm20) REVERT: B 987 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8276 (mp0) REVERT: B 999 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 1105 ASP cc_start: 0.8943 (t0) cc_final: 0.8713 (t0) REVERT: B 1237 GLN cc_start: 0.8632 (pt0) cc_final: 0.8371 (pt0) REVERT: B 1354 GLU cc_start: 0.8793 (tt0) cc_final: 0.8372 (tm-30) REVERT: B 1578 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8236 (mtp180) REVERT: C 71 ASP cc_start: 0.8948 (p0) cc_final: 0.8668 (p0) REVERT: C 343 ASP cc_start: 0.8119 (p0) cc_final: 0.7913 (p0) REVERT: C 797 ASP cc_start: 0.9256 (t0) cc_final: 0.8999 (t0) REVERT: C 885 SER cc_start: 0.9421 (t) cc_final: 0.9183 (p) REVERT: C 1337 GLU cc_start: 0.8906 (tt0) cc_final: 0.8535 (tt0) REVERT: C 1420 ASN cc_start: 0.8610 (m-40) cc_final: 0.8353 (m-40) REVERT: D 460 ASP cc_start: 0.8869 (t0) cc_final: 0.8574 (t70) REVERT: D 466 ASP cc_start: 0.9102 (t0) cc_final: 0.8849 (t0) REVERT: D 720 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8723 (mtt) REVERT: D 1150 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: D 1170 ASP cc_start: 0.8638 (m-30) cc_final: 0.8303 (m-30) REVERT: E 978 GLU cc_start: 0.8488 (pm20) cc_final: 0.8127 (pm20) REVERT: E 987 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8294 (mp0) REVERT: E 1105 ASP cc_start: 0.9011 (t0) cc_final: 0.8795 (t0) REVERT: E 1237 GLN cc_start: 0.8657 (pt0) cc_final: 0.8406 (pt0) REVERT: E 1354 GLU cc_start: 0.8724 (tt0) cc_final: 0.8316 (tm-30) REVERT: F 343 ASP cc_start: 0.8145 (p0) cc_final: 0.7925 (p0) REVERT: F 797 ASP cc_start: 0.9281 (t0) cc_final: 0.8997 (t0) REVERT: F 885 SER cc_start: 0.9437 (t) cc_final: 0.9199 (p) REVERT: F 1091 ASP cc_start: 0.7754 (p0) cc_final: 0.7464 (p0) REVERT: F 1420 ASN cc_start: 0.8604 (m-40) cc_final: 0.8328 (m-40) outliers start: 131 outliers final: 61 residues processed: 650 average time/residue: 1.1262 time to fit residues: 1050.4819 Evaluate side-chains 540 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 473 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1324 SER Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1578 ARG Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1308 ASP Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1406 SER Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1018 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 10.0000 chunk 648 optimal weight: 0.2980 chunk 447 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 411 optimal weight: 8.9990 chunk 579 optimal weight: 9.9990 chunk 865 optimal weight: 0.6980 chunk 916 optimal weight: 9.9990 chunk 452 optimal weight: 8.9990 chunk 820 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 ASN B 663 ASN B1050 HIS B1452 ASN C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 409 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1167 ASN D1237 GLN D1392 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 623 ASN E 663 ASN E1050 HIS ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1392 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 71646 Z= 0.374 Angle : 0.599 10.605 98034 Z= 0.328 Chirality : 0.048 0.171 11682 Planarity : 0.004 0.049 13194 Dihedral : 5.110 65.764 9892 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.30 % Allowed : 12.03 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 (0.08), residues: 9468 helix: -2.14 (0.17), residues: 692 sheet: 0.64 (0.10), residues: 2828 loop : -0.83 (0.07), residues: 5948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E1275 HIS 0.005 0.001 HIS F 279 PHE 0.022 0.002 PHE A 124 TYR 0.018 0.002 TYR F1268 ARG 0.007 0.001 ARG D1578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 503 time to evaluate : 6.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASP cc_start: 0.8954 (t0) cc_final: 0.8670 (t70) REVERT: A 466 ASP cc_start: 0.9135 (t0) cc_final: 0.8880 (t0) REVERT: A 720 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8791 (mtt) REVERT: A 1150 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: A 1170 ASP cc_start: 0.8672 (m-30) cc_final: 0.8329 (m-30) REVERT: B 472 GLN cc_start: 0.8188 (mt0) cc_final: 0.7928 (mm110) REVERT: B 606 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9145 (tp30) REVERT: B 978 GLU cc_start: 0.8710 (pm20) cc_final: 0.8373 (pm20) REVERT: B 987 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8276 (mp0) REVERT: B 999 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7808 (mm-30) REVERT: B 1019 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6933 (t0) REVERT: B 1105 ASP cc_start: 0.8861 (t0) cc_final: 0.8651 (t0) REVERT: B 1354 GLU cc_start: 0.8772 (tt0) cc_final: 0.8311 (tm-30) REVERT: C 71 ASP cc_start: 0.9065 (p0) cc_final: 0.8836 (p0) REVERT: C 720 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: C 797 ASP cc_start: 0.9277 (t0) cc_final: 0.9014 (t0) REVERT: C 1420 ASN cc_start: 0.8726 (m-40) cc_final: 0.8487 (m-40) REVERT: C 1573 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: D 460 ASP cc_start: 0.8958 (t0) cc_final: 0.8684 (t70) REVERT: D 466 ASP cc_start: 0.9129 (t0) cc_final: 0.8866 (t0) REVERT: D 720 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8822 (mtt) REVERT: D 1150 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: D 1170 ASP cc_start: 0.8704 (m-30) cc_final: 0.8334 (m-30) REVERT: E 342 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7896 (tt0) REVERT: E 978 GLU cc_start: 0.8692 (pm20) cc_final: 0.8344 (pm20) REVERT: E 987 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8302 (mp0) REVERT: E 1105 ASP cc_start: 0.8958 (t0) cc_final: 0.8734 (t0) REVERT: E 1354 GLU cc_start: 0.8762 (tt0) cc_final: 0.8277 (tm-30) REVERT: E 1548 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7401 (pp) REVERT: F 797 ASP cc_start: 0.9308 (t0) cc_final: 0.9025 (t0) REVERT: F 1420 ASN cc_start: 0.8701 (m-40) cc_final: 0.8414 (m-40) REVERT: F 1573 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7657 (pt0) outliers start: 181 outliers final: 93 residues processed: 635 average time/residue: 1.1889 time to fit residues: 1079.4196 Evaluate side-chains 550 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 448 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1019 ASP Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1578 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1406 SER Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 711 ASP Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1194 SER Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1548 ILE Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1138 GLU Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1406 SER Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1548 ILE 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 721 ASP Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1018 LEU Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1406 SER Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 7.9990 chunk 520 optimal weight: 0.0050 chunk 13 optimal weight: 6.9990 chunk 682 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 781 optimal weight: 7.9990 chunk 633 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 467 optimal weight: 10.0000 chunk 822 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 364 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1452 ASN C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 583 GLN ** C 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN C1577 HIS ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN D 409 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN F 623 ASN F1325 ASN F1577 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 71646 Z= 0.371 Angle : 0.590 9.990 98034 Z= 0.323 Chirality : 0.048 0.179 11682 Planarity : 0.004 0.051 13194 Dihedral : 5.094 65.420 9892 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.52 % Allowed : 12.44 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.75 (0.08), residues: 9468 helix: -2.10 (0.17), residues: 692 sheet: 0.61 (0.10), residues: 2808 loop : -0.86 (0.07), residues: 5968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C1275 HIS 0.005 0.001 HIS B1050 PHE 0.019 0.002 PHE D 124 TYR 0.019 0.002 TYR C1268 ARG 0.004 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 485 time to evaluate : 6.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASP cc_start: 0.9147 (t0) cc_final: 0.8906 (t0) REVERT: A 720 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8822 (mtt) REVERT: A 1138 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8595 (mm-30) REVERT: A 1139 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: A 1150 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: A 1170 ASP cc_start: 0.8678 (m-30) cc_final: 0.8316 (m-30) REVERT: A 1407 ASP cc_start: 0.8885 (t70) cc_final: 0.8539 (p0) REVERT: B 342 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7946 (tt0) REVERT: B 472 GLN cc_start: 0.8198 (mt0) cc_final: 0.7909 (mm110) REVERT: B 592 ASP cc_start: 0.7825 (t0) cc_final: 0.7601 (t0) REVERT: B 606 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9157 (tp30) REVERT: B 978 GLU cc_start: 0.8739 (pm20) cc_final: 0.8390 (pm20) REVERT: B 987 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8258 (mp0) REVERT: B 1105 ASP cc_start: 0.8875 (t0) cc_final: 0.8635 (t0) REVERT: B 1354 GLU cc_start: 0.8796 (tt0) cc_final: 0.8408 (tm-30) REVERT: B 1578 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8588 (mtp180) REVERT: C 66 ASP cc_start: 0.8651 (t0) cc_final: 0.8378 (t0) REVERT: C 797 ASP cc_start: 0.9294 (t0) cc_final: 0.9021 (t0) REVERT: C 1070 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8738 (t) REVERT: D 720 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8836 (mtt) REVERT: D 1150 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: D 1170 ASP cc_start: 0.8708 (m-30) cc_final: 0.8338 (m-30) REVERT: E 342 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7861 (tt0) REVERT: E 592 ASP cc_start: 0.7811 (t0) cc_final: 0.7602 (t0) REVERT: E 978 GLU cc_start: 0.8736 (pm20) cc_final: 0.8381 (pm20) REVERT: E 987 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8292 (mp0) REVERT: E 1105 ASP cc_start: 0.8933 (t0) cc_final: 0.8715 (t0) REVERT: E 1352 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: E 1354 GLU cc_start: 0.8768 (tt0) cc_final: 0.8355 (tm-30) REVERT: F 797 ASP cc_start: 0.9314 (t0) cc_final: 0.9038 (t0) REVERT: F 1070 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8779 (t) REVERT: F 1090 MET cc_start: 0.8580 (tmm) cc_final: 0.8377 (tmt) REVERT: F 1403 GLU cc_start: 0.8734 (pm20) cc_final: 0.8427 (pm20) REVERT: F 1420 ASN cc_start: 0.8720 (m-40) cc_final: 0.8448 (m-40) REVERT: F 1573 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7585 (pt0) outliers start: 198 outliers final: 106 residues processed: 631 average time/residue: 1.1734 time to fit residues: 1063.4150 Evaluate side-chains 569 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 453 time to evaluate : 7.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1138 GLU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1194 SER Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1336 LEU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1405 ASP Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1578 ARG Chi-restraints excluded: chain C residue 67 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 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1070 THR Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1262 ASN Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1406 SER Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1223 VAL Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1406 SER Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1548 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1138 GLU Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1323 LEU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1406 SER Chi-restraints excluded: chain E residue 1520 VAL 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 275 VAL Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1070 THR Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1406 SER Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 5.9990 chunk 825 optimal weight: 8.9990 chunk 181 optimal weight: 0.1980 chunk 538 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 917 optimal weight: 2.9990 chunk 761 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 481 optimal weight: 0.7980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN A 364 GLN A 409 GLN A 472 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 583 GLN C 623 ASN C1325 ASN C1452 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN D 409 GLN D 472 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 71646 Z= 0.193 Angle : 0.512 8.730 98034 Z= 0.280 Chirality : 0.045 0.162 11682 Planarity : 0.003 0.050 13194 Dihedral : 4.707 63.579 9892 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.01 % Allowed : 13.01 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 (0.08), residues: 9468 helix: -1.91 (0.18), residues: 692 sheet: 0.66 (0.10), residues: 2880 loop : -0.76 (0.08), residues: 5896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F1275 HIS 0.003 0.001 HIS B1050 PHE 0.014 0.001 PHE D 102 TYR 0.014 0.001 TYR C1268 ARG 0.003 0.000 ARG D1578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 521 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASP cc_start: 0.9027 (t0) cc_final: 0.8693 (t70) REVERT: A 466 ASP cc_start: 0.9142 (t0) cc_final: 0.8929 (t0) REVERT: A 720 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8687 (mtt) REVERT: A 1138 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8481 (mm-30) REVERT: A 1139 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: A 1150 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: A 1170 ASP cc_start: 0.8662 (m-30) cc_final: 0.8336 (m-30) REVERT: A 1407 ASP cc_start: 0.8913 (t70) cc_final: 0.8692 (p0) REVERT: B 472 GLN cc_start: 0.8205 (mt0) cc_final: 0.7922 (mm110) REVERT: B 606 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9128 (tp30) REVERT: B 978 GLU cc_start: 0.8723 (pm20) cc_final: 0.8362 (pm20) REVERT: B 987 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8270 (mp0) REVERT: B 1105 ASP cc_start: 0.8855 (t0) cc_final: 0.8639 (t0) REVERT: B 1354 GLU cc_start: 0.8811 (tt0) cc_final: 0.8416 (tm-30) REVERT: B 1405 ASP cc_start: 0.9276 (m-30) cc_final: 0.8978 (m-30) REVERT: B 1578 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8524 (mtp180) REVERT: C 71 ASP cc_start: 0.8994 (p0) cc_final: 0.8762 (p0) REVERT: C 797 ASP cc_start: 0.9264 (t0) cc_final: 0.9005 (t0) REVERT: C 1548 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7530 (pp) REVERT: D 143 GLU cc_start: 0.7638 (tp30) cc_final: 0.7424 (tp30) REVERT: D 460 ASP cc_start: 0.9019 (t0) cc_final: 0.8737 (t70) REVERT: D 720 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8691 (mtt) REVERT: D 1150 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: D 1170 ASP cc_start: 0.8684 (m-30) cc_final: 0.8344 (m-30) REVERT: D 1488 GLU cc_start: 0.7558 (mp0) cc_final: 0.6936 (mp0) REVERT: E 978 GLU cc_start: 0.8707 (pm20) cc_final: 0.8349 (pm20) REVERT: E 987 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8293 (mp0) REVERT: E 1105 ASP cc_start: 0.8912 (t0) cc_final: 0.8694 (t0) REVERT: E 1352 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: E 1354 GLU cc_start: 0.8795 (tt0) cc_final: 0.8356 (tm-30) REVERT: F 797 ASP cc_start: 0.9298 (t0) cc_final: 0.9027 (t0) REVERT: F 1090 MET cc_start: 0.8543 (tmm) cc_final: 0.8342 (tmt) REVERT: F 1420 ASN cc_start: 0.8641 (m-40) cc_final: 0.8388 (m-40) REVERT: F 1548 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7531 (pp) outliers start: 158 outliers final: 84 residues processed: 639 average time/residue: 1.1014 time to fit residues: 1018.6005 Evaluate side-chains 553 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 460 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1578 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1406 SER Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1548 ILE Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1194 SER Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1548 ILE 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 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1019 ASP Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1323 LEU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1548 ILE Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 522 optimal weight: 5.9990 chunk 669 optimal weight: 2.9990 chunk 518 optimal weight: 6.9990 chunk 772 optimal weight: 8.9990 chunk 512 optimal weight: 6.9990 chunk 913 optimal weight: 20.0000 chunk 571 optimal weight: 9.9990 chunk 557 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A1392 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1452 ASN C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C1083 ASN C1325 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D1050 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 71646 Z= 0.405 Angle : 0.611 9.893 98034 Z= 0.333 Chirality : 0.048 0.172 11682 Planarity : 0.004 0.058 13194 Dihedral : 5.118 63.553 9892 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.27 % Allowed : 13.58 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.73 (0.08), residues: 9468 helix: -1.95 (0.17), residues: 692 sheet: 0.62 (0.10), residues: 2780 loop : -0.86 (0.07), residues: 5996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C1275 HIS 0.004 0.001 HIS A1050 PHE 0.019 0.002 PHE A 102 TYR 0.017 0.002 TYR A 763 ARG 0.004 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 463 time to evaluate : 6.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASP cc_start: 0.9178 (t0) cc_final: 0.8961 (t0) REVERT: A 720 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8822 (mtt) REVERT: A 1139 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: A 1150 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: A 1170 ASP cc_start: 0.8693 (m-30) cc_final: 0.8342 (m-30) REVERT: A 1573 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: B 342 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8015 (tt0) REVERT: B 606 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9164 (tp30) REVERT: B 978 GLU cc_start: 0.8773 (pm20) cc_final: 0.8419 (pm20) REVERT: B 1105 ASP cc_start: 0.8874 (t0) cc_final: 0.8655 (t0) REVERT: B 1352 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: B 1354 GLU cc_start: 0.8786 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 1578 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8719 (mtp180) REVERT: C 797 ASP cc_start: 0.9298 (t0) cc_final: 0.9024 (t0) REVERT: C 1302 ASP cc_start: 0.9301 (OUTLIER) cc_final: 0.9001 (p0) REVERT: C 1548 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7582 (pp) REVERT: D 143 GLU cc_start: 0.7293 (tp30) cc_final: 0.7044 (tp30) REVERT: D 720 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8855 (mtt) REVERT: D 1150 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: D 1170 ASP cc_start: 0.8746 (m-30) cc_final: 0.8380 (m-30) REVERT: E 342 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7948 (tt0) REVERT: E 978 GLU cc_start: 0.8782 (pm20) cc_final: 0.8421 (pm20) REVERT: E 1352 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: E 1354 GLU cc_start: 0.8774 (tt0) cc_final: 0.8356 (tm-30) REVERT: F 797 ASP cc_start: 0.9329 (t0) cc_final: 0.9040 (t0) REVERT: F 1090 MET cc_start: 0.8545 (tmm) cc_final: 0.8280 (tmt) REVERT: F 1420 ASN cc_start: 0.8756 (m-40) cc_final: 0.8497 (m-40) REVERT: F 1548 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7589 (pp) REVERT: F 1573 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7606 (pt0) outliers start: 179 outliers final: 106 residues processed: 596 average time/residue: 1.1602 time to fit residues: 991.7325 Evaluate side-chains 563 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 444 time to evaluate : 5.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1578 ARG 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 254 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1150 GLU 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 1302 ASP Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1384 ILE Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1524 ASP Chi-restraints excluded: chain C residue 1548 ILE Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1019 ASP Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL 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 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1000 ILE Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1138 GLU Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1262 ASN Chi-restraints excluded: chain F residue 1302 ASP Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1384 ILE Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1524 ASP Chi-restraints excluded: chain F residue 1548 ILE Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 545 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 580 optimal weight: 2.9990 chunk 622 optimal weight: 6.9990 chunk 451 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 718 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 583 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 583 GLN C1325 ASN C1452 ASN D 38 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 583 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 71646 Z= 0.310 Angle : 0.570 9.784 98034 Z= 0.310 Chirality : 0.047 0.162 11682 Planarity : 0.004 0.062 13194 Dihedral : 4.982 63.108 9892 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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 (0.08), residues: 9468 helix: -1.87 (0.18), residues: 678 sheet: 0.64 (0.10), residues: 2812 loop : -0.85 (0.07), residues: 5978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1275 HIS 0.004 0.001 HIS C1050 PHE 0.018 0.001 PHE A 102 TYR 0.015 0.002 TYR F1383 ARG 0.006 0.000 ARG A 802 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 463 time to evaluate : 6.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASP cc_start: 0.9168 (t0) cc_final: 0.8956 (t0) REVERT: A 720 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8769 (mtt) REVERT: A 1138 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8655 (mm-30) REVERT: A 1150 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: A 1170 ASP cc_start: 0.8657 (m-30) cc_final: 0.8292 (m-30) REVERT: A 1407 ASP cc_start: 0.8888 (t70) cc_final: 0.8626 (p0) REVERT: A 1524 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: B 342 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8018 (tt0) REVERT: B 592 ASP cc_start: 0.7810 (t0) cc_final: 0.7557 (t0) REVERT: B 606 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9160 (tp30) REVERT: B 978 GLU cc_start: 0.8763 (pm20) cc_final: 0.8405 (pm20) REVERT: B 1105 ASP cc_start: 0.8854 (t0) cc_final: 0.8632 (t0) REVERT: B 1352 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 1354 GLU cc_start: 0.8801 (tt0) cc_final: 0.8415 (tm-30) REVERT: B 1578 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8686 (mtp180) REVERT: C 71 ASP cc_start: 0.8976 (p0) cc_final: 0.8762 (t0) REVERT: C 797 ASP cc_start: 0.9291 (t0) cc_final: 0.9023 (t0) REVERT: C 1032 ASP cc_start: 0.8138 (m-30) cc_final: 0.7708 (p0) REVERT: C 1302 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.8977 (p0) REVERT: C 1548 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7568 (pp) REVERT: D 421 GLU cc_start: 0.7582 (mp0) cc_final: 0.7365 (mp0) REVERT: D 720 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8779 (mtt) REVERT: D 1150 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: D 1170 ASP cc_start: 0.8670 (m-30) cc_final: 0.8317 (m-30) REVERT: D 1524 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: E 342 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7906 (tt0) REVERT: E 592 ASP cc_start: 0.7828 (t0) cc_final: 0.7579 (t0) REVERT: E 978 GLU cc_start: 0.8744 (pm20) cc_final: 0.8386 (pm20) REVERT: E 1105 ASP cc_start: 0.8863 (t0) cc_final: 0.8631 (t0) REVERT: E 1352 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: E 1354 GLU cc_start: 0.8780 (tt0) cc_final: 0.8358 (tm-30) REVERT: F 797 ASP cc_start: 0.9325 (t0) cc_final: 0.9043 (t0) REVERT: F 1032 ASP cc_start: 0.8091 (m-30) cc_final: 0.7703 (p0) REVERT: F 1090 MET cc_start: 0.8547 (tmm) cc_final: 0.8295 (tmt) REVERT: F 1302 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.9007 (p0) REVERT: F 1420 ASN cc_start: 0.8750 (m-40) cc_final: 0.8493 (m-40) REVERT: F 1548 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7547 (pp) outliers start: 163 outliers final: 113 residues processed: 587 average time/residue: 1.1312 time to fit residues: 963.2566 Evaluate side-chains 568 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 442 time to evaluate : 6.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1138 GLU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1194 SER Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain B residue 1578 ARG Chi-restraints excluded: chain C residue 67 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 254 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1070 THR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1302 ASP Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1384 ILE Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1524 ASP Chi-restraints excluded: chain C residue 1548 ILE Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1548 ILE 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 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1138 GLU Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1323 LEU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1302 ASP Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1384 ILE Chi-restraints excluded: chain F residue 1397 LEU Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1524 ASP Chi-restraints excluded: chain F residue 1548 ILE Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 6.9990 chunk 875 optimal weight: 5.9990 chunk 798 optimal weight: 2.9990 chunk 851 optimal weight: 8.9990 chunk 512 optimal weight: 6.9990 chunk 370 optimal weight: 7.9990 chunk 668 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 769 optimal weight: 9.9990 chunk 805 optimal weight: 6.9990 chunk 848 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 583 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C1325 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 583 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 71646 Z= 0.311 Angle : 0.574 9.767 98034 Z= 0.312 Chirality : 0.047 0.162 11682 Planarity : 0.004 0.057 13194 Dihedral : 4.814 22.717 9888 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.20 % Allowed : 14.19 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.70 (0.08), residues: 9468 helix: -1.91 (0.18), residues: 692 sheet: 0.64 (0.10), residues: 2812 loop : -0.85 (0.07), residues: 5964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1275 HIS 0.004 0.001 HIS E1050 PHE 0.017 0.001 PHE A 102 TYR 0.015 0.001 TYR C1383 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 453 time to evaluate : 6.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ASP cc_start: 0.9170 (t0) cc_final: 0.8955 (t0) REVERT: A 720 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8784 (mtt) REVERT: A 737 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8542 (mtt-85) REVERT: A 1138 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 1150 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: A 1170 ASP cc_start: 0.8632 (m-30) cc_final: 0.8283 (m-30) REVERT: A 1232 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7235 (mpp-170) REVERT: A 1407 ASP cc_start: 0.8891 (t70) cc_final: 0.8675 (p0) REVERT: A 1524 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: A 1573 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: B 342 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8021 (tt0) REVERT: B 592 ASP cc_start: 0.6991 (t0) cc_final: 0.6735 (t0) REVERT: B 606 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9160 (tp30) REVERT: B 978 GLU cc_start: 0.8763 (pm20) cc_final: 0.8404 (pm20) REVERT: B 1019 ASP cc_start: 0.7176 (t0) cc_final: 0.6975 (t0) REVERT: B 1352 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: B 1354 GLU cc_start: 0.8807 (tt0) cc_final: 0.8402 (tm-30) REVERT: C 71 ASP cc_start: 0.8979 (p0) cc_final: 0.8774 (t0) REVERT: C 797 ASP cc_start: 0.9288 (t0) cc_final: 0.9020 (t0) REVERT: C 1032 ASP cc_start: 0.8168 (m-30) cc_final: 0.7712 (p0) REVERT: C 1302 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8943 (p0) REVERT: C 1548 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7580 (pp) REVERT: D 421 GLU cc_start: 0.7632 (mp0) cc_final: 0.7414 (mp0) REVERT: D 720 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8797 (mtt) REVERT: D 737 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8667 (mtt180) REVERT: D 1150 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: D 1170 ASP cc_start: 0.8704 (m-30) cc_final: 0.8347 (m-30) REVERT: D 1232 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7184 (mpp-170) REVERT: D 1524 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: E 342 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7877 (tt0) REVERT: E 592 ASP cc_start: 0.6999 (t0) cc_final: 0.6743 (t0) REVERT: E 978 GLU cc_start: 0.8726 (pm20) cc_final: 0.8362 (pm20) REVERT: E 1105 ASP cc_start: 0.8847 (t0) cc_final: 0.8598 (t0) REVERT: E 1352 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: E 1354 GLU cc_start: 0.8789 (tt0) cc_final: 0.8364 (tm-30) REVERT: F 797 ASP cc_start: 0.9323 (t0) cc_final: 0.9039 (t0) REVERT: F 1032 ASP cc_start: 0.8112 (m-30) cc_final: 0.7679 (p0) REVERT: F 1090 MET cc_start: 0.8570 (tmm) cc_final: 0.8338 (tmt) REVERT: F 1302 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.9010 (p0) REVERT: F 1420 ASN cc_start: 0.8748 (m-40) cc_final: 0.8487 (m-40) REVERT: F 1548 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7540 (pp) outliers start: 173 outliers final: 124 residues processed: 587 average time/residue: 1.1348 time to fit residues: 956.7418 Evaluate side-chains 578 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 437 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 583 GLN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1524 ASP Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1573 GLU 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 252 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1082 GLU Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1138 GLU Chi-restraints excluded: chain B residue 1194 SER Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1323 LEU Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1372 ASP Chi-restraints excluded: chain B residue 1384 ILE Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain B residue 1524 ASP Chi-restraints excluded: chain C residue 67 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 254 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1070 THR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1150 GLU Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1302 ASP Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1384 ILE Chi-restraints excluded: chain C residue 1397 LEU Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1524 ASP Chi-restraints excluded: chain C residue 1548 ILE Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 737 ARG Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1232 ARG Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1524 ASP Chi-restraints excluded: chain D residue 1548 ILE 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 252 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 766 VAL Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 836 SER Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain E residue 904 THR Chi-restraints excluded: chain E residue 1021 THR Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1138 GLU Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1323 LEU Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1372 ASP Chi-restraints excluded: chain E residue 1384 ILE Chi-restraints excluded: chain E residue 1405 ASP Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 721 ASP Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1019 ASP Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1070 THR Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1150 GLU Chi-restraints excluded: chain F residue 1201 LEU Chi-restraints excluded: chain F residue 1207 GLN Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1302 ASP Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1384 ILE Chi-restraints excluded: chain F residue 1452 ASN Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1524 ASP Chi-restraints excluded: chain F residue 1548 ILE Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 2.9990 chunk 900 optimal weight: 0.0050 chunk 549 optimal weight: 1.9990 chunk 427 optimal weight: 9.9990 chunk 625 optimal weight: 6.9990 chunk 944 optimal weight: 20.0000 chunk 869 optimal weight: 0.9980 chunk 752 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 580 optimal weight: 0.9990 chunk 461 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 409 GLN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1452 ASN C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C1325 ASN C1452 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN D 409 GLN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 71646 Z= 0.175 Angle : 0.519 9.029 98034 Z= 0.282 Chirality : 0.045 0.170 11682 Planarity : 0.003 0.054 13194 Dihedral : 4.453 23.099 9888 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 15.13 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % 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: -0.53 (0.08), residues: 9468 helix: -1.78 (0.18), residues: 692 sheet: 0.72 (0.10), residues: 2860 loop : -0.72 (0.08), residues: 5916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1275 HIS 0.003 0.001 HIS E1050 PHE 0.015 0.001 PHE D 524 TYR 0.013 0.001 TYR F1383 ARG 0.003 0.000 ARG B1578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 475 time to evaluate : 5.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASP cc_start: 0.8956 (t0) cc_final: 0.8704 (t70) REVERT: A 720 MET cc_start: 0.9065 (mmm) cc_final: 0.8641 (mtt) REVERT: A 737 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8494 (mtt-85) REVERT: A 1138 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 1139 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: A 1150 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: A 1170 ASP cc_start: 0.8621 (m-30) cc_final: 0.8296 (m-30) REVERT: A 1232 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7187 (mpp-170) REVERT: A 1573 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: B 592 ASP cc_start: 0.7318 (t0) cc_final: 0.7067 (t0) REVERT: B 606 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9115 (tp30) REVERT: B 978 GLU cc_start: 0.8733 (pm20) cc_final: 0.8329 (pm20) REVERT: B 1105 ASP cc_start: 0.8782 (t0) cc_final: 0.8524 (t0) REVERT: B 1352 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 1354 GLU cc_start: 0.8817 (tt0) cc_final: 0.8396 (tm-30) REVERT: C 71 ASP cc_start: 0.8911 (p0) cc_final: 0.8707 (t0) REVERT: C 797 ASP cc_start: 0.9256 (t0) cc_final: 0.9007 (t0) REVERT: C 1032 ASP cc_start: 0.8262 (m-30) cc_final: 0.7809 (p0) REVERT: C 1104 SER cc_start: 0.9093 (p) cc_final: 0.8582 (m) REVERT: C 1548 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7538 (pp) REVERT: D 460 ASP cc_start: 0.9024 (t0) cc_final: 0.8691 (t70) REVERT: D 720 MET cc_start: 0.9060 (mmm) cc_final: 0.8663 (mtt) REVERT: D 737 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8619 (mtt180) REVERT: D 1150 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: D 1170 ASP cc_start: 0.8689 (m-30) cc_final: 0.8374 (m-30) REVERT: D 1488 GLU cc_start: 0.7567 (mp0) cc_final: 0.6965 (mp0) REVERT: E 342 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7938 (tt0) REVERT: E 592 ASP cc_start: 0.6951 (t0) cc_final: 0.6709 (t0) REVERT: E 978 GLU cc_start: 0.8700 (pm20) cc_final: 0.8290 (pm20) REVERT: E 1019 ASP cc_start: 0.7073 (t0) cc_final: 0.6858 (t0) REVERT: E 1105 ASP cc_start: 0.8832 (t0) cc_final: 0.8566 (t0) REVERT: E 1352 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: E 1354 GLU cc_start: 0.8807 (tt0) cc_final: 0.8350 (tm-30) REVERT: F 797 ASP cc_start: 0.9288 (t0) cc_final: 0.9010 (t0) REVERT: F 1032 ASP cc_start: 0.8219 (m-30) cc_final: 0.7749 (p0) REVERT: F 1090 MET cc_start: 0.8562 (tmm) cc_final: 0.8358 (tmt) REVERT: F 1302 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.9006 (p0) REVERT: F 1420 ASN cc_start: 0.8647 (m-40) cc_final: 0.8377 (m-40) REVERT: F 1548 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7511 (pp) outliers start: 112 outliers final: 65 residues processed: 558 average time/residue: 1.1647 time to fit residues: 935.4424 Evaluate side-chains 521 residues out of total 7872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 444 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1372 ASP Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1405 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1573 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 904 THR Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1207 GLN Chi-restraints excluded: chain B residue 1352 GLU Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain B residue 1452 ASN Chi-restraints excluded: chain B residue 1520 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 1055 THR Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1207 GLN Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1372 ASP Chi-restraints excluded: chain C residue 1452 ASN Chi-restraints excluded: chain C residue 1520 VAL Chi-restraints excluded: chain C residue 1524 ASP Chi-restraints excluded: chain C residue 1548 ILE Chi-restraints excluded: chain C residue 1573 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 737 ARG Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1372 ASP Chi-restraints excluded: chain D residue 1398 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 692 THR Chi-restraints excluded: chain E residue 711 ASP Chi-restraints excluded: chain E residue 815 THR Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain E residue 1179 THR Chi-restraints excluded: chain E residue 1194 SER Chi-restraints excluded: chain E residue 1207 GLN Chi-restraints excluded: chain E residue 1352 GLU Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1520 VAL Chi-restraints excluded: chain E residue 1524 ASP Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 583 GLN Chi-restraints excluded: chain F residue 843 VAL Chi-restraints excluded: chain F residue 904 THR Chi-restraints excluded: chain F residue 917 SER Chi-restraints excluded: chain F residue 1055 THR Chi-restraints excluded: chain F residue 1224 THR Chi-restraints excluded: chain F residue 1302 ASP Chi-restraints excluded: chain F residue 1372 ASP Chi-restraints excluded: chain F residue 1520 VAL Chi-restraints excluded: chain F residue 1524 ASP Chi-restraints excluded: chain F residue 1548 ILE Chi-restraints excluded: chain F residue 1573 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 0.9980 chunk 801 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 693 optimal weight: 10.0000 chunk 111 optimal weight: 0.0030 chunk 208 optimal weight: 9.9990 chunk 753 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 773 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A 617 ASN ** A 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1325 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 617 ASN ** D 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1325 ASN F1452 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078605 restraints weight = 144608.082| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.51 r_work: 0.3010 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 71646 Z= 0.244 Angle : 0.696 59.188 98034 Z= 0.396 Chirality : 0.047 0.907 11682 Planarity : 0.005 0.215 13194 Dihedral : 4.490 39.847 9888 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.22 % Allowed : 15.47 % Favored : 83.31 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.52 (0.08), residues: 9468 helix: -1.78 (0.18), residues: 692 sheet: 0.72 (0.10), residues: 2860 loop : -0.71 (0.08), residues: 5916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1275 HIS 0.012 0.001 HIS B1072 PHE 0.014 0.001 PHE D 524 TYR 0.013 0.001 TYR F1383 ARG 0.003 0.000 ARG A 744 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19788.28 seconds wall clock time: 341 minutes 30.04 seconds (20490.04 seconds total)